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Basic information

Entry
Database: PDB / ID: 1bkv
TitleCOLLAGEN
ComponentsT3-785
KeywordsSTRUCTURAL PROTEIN / COLLAGEN / HYDROXYPROLINE / HYDROGEN BONDING / TRIPLE HELIX / TYPE III COLLAGEN
Function / homologyACETIC ACID
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKramer, R.Z. / Bella, J. / Mayville, P. / Brodsky, B. / Berman, H.M.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Sequence dependent conformational variations of collagen triple-helical structure.
Authors: Kramer, R.Z. / Bella, J. / Mayville, P. / Brodsky, B. / Berman, H.M.
History
DepositionJul 13, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T3-785
B: T3-785
C: T3-785
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3618
Polymers8,0613
Non-polymers3005
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-27 kcal/mol
Surface area5260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.090, 15.629, 39.715
Angle α, β, γ (deg.)90.00, 104.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-401-

ACY

21B-401-

ACY

31B-405-

ACY

41B-405-

ACY

51A-134-

HOH

61A-189-

HOH

71A-211-

HOH

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Components

#1: Protein/peptide T3-785


Mass: 2686.908 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: MODEL PEPTIDE CONTAINING BIOLOGICAL SEQUENCE WAS CHEMICALLY SYNTHESIZED
#2: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROGEN BONDS BETWEEN PEPTIDE CHAINS FOLLOW THE RICH AND CRICK MODEL II FOR COLLAGEN.
Nonpolymer detailsTWO ACETIC ACID MOLECULES SIT ON A CRYSTALLOGRAPHIC TWO FOLD. AS A RESULT THE ASYMMETRIC UNIT FOR ...TWO ACETIC ACID MOLECULES SIT ON A CRYSTALLOGRAPHIC TWO FOLD. AS A RESULT THE ASYMMETRIC UNIT FOR THESE TWO ACETIC ACIDS CONTAIN ONLY ONE OXYGEN ATOM EACH.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 43.5 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110.0 mg/mlpeptide1drop
215 %PEG40001drop
30.05 Macetic acid1drop
40.05 MTris-HCl1drop
50.1 M1dropLi2SO4
630 %PEG40001reservoir
70.1 MTris-HCl1reservoir
80.2 M1reservoirLiSO4

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 4853 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.053
Reflection shellResolution: 2→2.06 Å / Rmerge(I) obs: 0.133 / % possible all: 93
Reflection
*PLUS
% possible obs: 96 % / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 85 %

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Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IDEALIZED 7-FOLD TRIPLE HELIX

Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: ADDITIONAL PARAMETERS USED FOR HYDROXYPROLINE. THREE EXTREMELY STRONG REFLECTIONS (-3 1 1, 4 0 2, AND 5 1 0) WERE UNDERESTIMATED AND HENCE WERE EXCLUDED FROM REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 486 9.6 %RANDOM
Rwork0.228 ---
obs0.228 4643 92 %-
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.576 Å20 Å2-15.601 Å2
2--9.383 Å20 Å2
3----2.808 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms563 0 18 111 692
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.281 29 -
Rwork0.265 348 -
obs--90 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.02
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04

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