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- PDB-1wzb: Crystal structure of the collagen triple helix model [{HYP(R)-HYP... -

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Basic information

Entry
Database: PDB / ID: 1wzb
TitleCrystal structure of the collagen triple helix model [{HYP(R)-HYP(R)-GLY}10]3
ComponentsCollagen triple helix
KeywordsSTRUCTURAL PROTEIN / collagen stability / puckering / amino acid-preferences / triple helix
Function / homologySaimiri transformation-associated protein / extracellular matrix structural constituent conferring tensile strength / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / extracellular matrix organization / extracellular space / membrane / Saimiri transformation-associated protein
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKawahara, K. / Nakamura, S. / Nishi, Y. / Uchiyama, S. / Nishiuchi, Y. / Nakazawa, T. / Ohkubo, T. / Kobayashi, Y.
CitationJournal: Biochemistry / Year: 2005
Title: Effect of hydration on the stability of the collagen-like triple-helical structure of [4(R)-hydroxyprolyl-4(R)-hydroxyprolylglycine]10
Authors: Kawahara, K. / Nishi, Y. / Nakamura, S. / Uchiyama, S. / Nishiuchi, Y. / Nakazawa, T. / Ohkubo, T. / Kobayashi, Y.
History
DepositionMar 3, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen triple helix
B: Collagen triple helix
C: Collagen triple helix


Theoretical massNumber of molelcules
Total (without water)8,5523
Polymers8,5523
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-27 kcal/mol
Surface area5080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)18.405, 19.113, 90.961
Angle α, β, γ (deg.)90.00, 94.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Collagen triple helix


Mass: 2850.828 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The protein was chemically synthesized / References: UniProt: Q80BK4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 33.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: HHG from 23.0 mg/ml peptide solution, 20% PEG 4000, 20% isopropanol, 0.2M Tris HCL buffer, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→30.24 Å / Num. obs: 10316 / % possible obs: 98.2 % / Redundancy: 5.65 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 27.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.05 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 15.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CLYSTALCLEAR VER1.35data collection
CLYSTALCLEAR VER1.35data reduction
ARP/wARPmodel building
REFMACrefinement
CrystalClearV. 1.35 (MSC/RIGAKU)data reduction
CrystalClearV. 1.35 (MSC/RIGAKU)data scaling
ACORNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K6F

1k6f


Resolution: 1.5→9.99 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20051 498 4.8 %RANDOM
Rwork0.16991 ---
all0.188 10271 --
obs0.17152 9772 98.22 %-
Displacement parametersBiso mean: 8.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms590 0 0 177 767

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