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
ATOM 319 N ASN 46 13.966 6.502 13.739 1.00 5.80 1CRN 388 ATOM 320 CA ASN 46 13.512 5.395 12.878 1.00 6.15 1CRN 389 ATOM 321 C ASN 46 13.311 5.853 11.455 1.00 6.61 1CRN 390 ATOM 322 O ASN 46 13.733 6.929 11.026 1.00 7.18 1CRN 391 ATOM 323 CB ASN 46 12.266 4.769 13.501 1.00 7.27 1CRN 392 ATOM 324 CG ASN 46 12.538 4.304 14.922 1.00 7.98 1CRN 393 ATOM 325 OD1 ASN 46 11.982 4.849 15.886 1.00 11.00 1CRN 394 ATOM 326 ND2 ASN 46 13.407 3.298 15.015 1.00 10.32 1CRN 395 ATOM 327 OXT ASN 46 12.703 4.973 10.746 1.00 7.86 1CRN 396 TER 328 ASN 46 1CRN 397 CONECT 20 19 282 1CRN 398 CONECT 26 25 229 1CRN 399 CONECT 116 115 188 1CRN 400 CONECT 188 116 187 1CRN 401 CONECT 229 26 228 1CRN 402 CONECT 282 20 281 1CRN 403 MASTER 62 0 0 2 2 1 0 6 327 1 6 4 1CRND 6 END 1CRN 405
When RasMol opens the 1crn.pdb file, the first two columns below are displayed in the command window. The additional third column indicates where the information occurs in this PDB file.
RasMol Category Crambin Entry PDB (cols 1-6) Label RasMol> Molecule name ....... CRAMBIN COMPND Classification ...... PLANT SEED PROTEIN HEADER Secondary Structure . PDB Data Records HELIX, SHEET, & TURN Brookhaven Code ..... 1CRN HEADER Number of Groups .... 46 SEQRES Number of Atoms ..... 327 ATOM 327 Number of Bonds ..... 3 SSBOND Number of Helices ... 2 HELIX Number of Strands ... 2 SHEET Number of Bonds ..... 334 RasMol>The Number of Bonds on the last line, is an internal RasMol calculation. The same information can be displayed at any time with the command, show information.
30-APR-81 is the original submission date for the coordinates.
1CRN is the Protein Data Bank ID code for this coordinate set.
REVDAT indicates the five revisions/ammendations made to this coordinate file. They are explained in REMARK 5-9 in the text. Four of these correspond to PDB files with new Brookhaven codes: 1CRNA, 1CRNB, 1CRNC, & 1CRND.
REFERENCE 1 is the primary reference for this model, as explained in REMARK 5; the primary reference is usually preceded by the JRNL label.
RESOLUTION corresponds to the amount of X-ray diffraction data included in the final model building and ultimately to the amount of atomic detail that will be interpreted in the electron density maps. Low resolution is >2.8Å; medium resolution is 1.8-2.8Å; and high resolution is <1.8Å. NMR models do not have an entry in this category.
The REFINEMENT method used here was RESTRAINED LEAST SQUARES. Some additional computational methods used for refinement (and cited in this section in other PDB files) are: CORELS, TNT, MD, etc.
The R-FACTOR is a measure of the overall quality of the model as compared to the experimental diffraction data. In this case, when the calculated intensities were compared to the observed data, the residual (rms) difference was 0.114 or 11.4%. NMR models do not have an entry in this category.
The four lines beginning with SEQRES 1 show the amino acid sequence of crambin from the N-terminal THR1 to the C-terminal ASN46. The same information (with residue numbers) can be displayed at any time with the command, show sequence.
If HETEROGEN atoms such as water, ligands, ions, etc. had been present in this file, they would have been listed here along with their names (HETNAM) and chemical formulas (FORMUL). The coordinates for these small molecules follow the protein data, each line beginning with HETATM in place of ATOM.
The HELIX, SHEET, and TURN lines record the authors' assignments of the secondary structure. These are used by RasMol, if present, to display and color the secondary structure. If absent from the PDB file, the DSSP algorithm of Kabsch and Sander [8] is used to calculate helices, sheets and turns.
For crambin, the first helix extends from Ile7 to Pro19; the second, from Glu23 to Thr30. For both helices, the notes on the HELIX lines indicate 310-helical geometry at the C-termini. The remaining residues are understood to be alpha-helix.
The SHEET lines identify two beta-strands extending from Thr1 to Cys4 and from Cys32 to Ile35.
The TURN extends from Pro41 to Tyr44. Consult the primary reference to learn which of the several regular turns this one is.
The three SSBOND lines were also assigned by the authors. They are disulfide bonds between Cys3-Cys40, Cys4-Cys32, and Cys16-Cys26. (See also the comments on CONECT lines below.)
The CRYST1 line reports the unit cell dimensions in Angstroms (A = 40.96Å, B = 18.65Å, and C = 22.52Å). The next three entries are the unit cell alpha, beta and gamma parameters. The last term on the line is the space group, P 21, i.e. P21. The same information can be displayed at any time with the command, show symmetry.
ATOM 1 starts the first of 327 lines of coordinates for crambin (of which, most have been deleted above). Atom number 1 is the amino-N (nitrogen) on Thr1.
CA indentifies atom number 2 as the C-alpha carbon. The other backbone atoms are C and O. The sidechain atoms are listed next: Thr1 has a CB (C-beta) and an OG (O-gamma).
THR is the Group (or residue) name. After picking this atom, the RasMol command line display would be:
Group (or residue) number in the sequence. THR1 can be selected using the command line atom expressions, "thr1", or "resno=1".
These three values are the X, Y, & Z coordinates (in Angstroms) of ATOM 5.
The occupancy value follows the X, Y, Z coordinates on each line; it is usually listed as 1.00. However, if a residue is found to occupy two positions in the structure, the corresponding values will be listed as a fraction (or explained by the authors, as was done here in REMARK 4 for Ile7, Ile25, and others).
The last datum on each coordinate line is the B-Factor. Also called the temperature factor, the B-Factor is a measure of the uncertainty of atomic position due both to thermal motion and crystal imperfections; the units are Å2. A value of 80Å2 corresponds roughly to a RMS (root mean square) uncertainty of ±1Å.
Each line in a PDB file is numbered sequentially. 1CRN 75 identifies this one as line 75.
ATOM 327, the last atom in the file, is the C-terminal oxygen of Thr46. It is uniquely designated as, OXT. However, it is chemically identical to another atom listed above. What is the atomno of its identical twin?
TER identifies the end of each polypeptide (or polynucleotide) chain. Crambin has only one chain.
The CONECT lines instruct RasMol to make covalent bonds between the atoms listed in each row. In this example, the disulfide bridges in crambin are specified. The first two columns list the SG and CB atoms by number of all six cysteines. The third column lists the SG of the cysteine to which each is bonded. Thus, the first line defines the Cys3-Cys40 disulfide bridge. The RasMol command, ssbonds controls the display of disulfide bonds. The CONECT records in a file can be discarded (and the connectivity recalculated by RasMol) by using the connect command.
END is the end-of-file statement for crystallographic models.
Typically, a PDB file will have information in this remark section on the following root mean square estimates:
RMS DEVIATIONS FROM IDEAL VALUES.
BOND LENGTHS (A) :
BOND ANGLES (DEGREES) :
DIHEDRAL ANGLES (DEGREES) :
As noted in REMARK 3, these authors deferred making these estimates until higher resolution refinement had been done.
Display of hetero atoms is controlled by the set hetero and related commands.
If the structure command is used, RasMol will discard the assignments in the PDB file and recalculate helices and sheets using the DSSP algorithm.
Atom: C 3 Group: THR 1
RasMol can label selected residues with a variety of name/number formats.
Check your answer by viewing the 1crn.pdb model in RasMol (or peek at the HTML text of this page).
However, NMR models often have several sets of coordinates in each PDB file. The sets can be distinguished by the MODEL1(-N) labels at the beginning, and the ENDM1(-N) labels at the end of each set. To manipulate multiple NMR models in PDB files, see the Manual description under Primitive Expressions.
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