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- PDB-6a0c: Structure of a triple-helix region of human collagen type III -

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Basic information

Entry
Database: PDB / ID: 6a0c
TitleStructure of a triple-helix region of human collagen type III
Componentscollagen type III peptide
KeywordsSTRUCTURAL PROTEIN / collagen
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsYang, X. / Zhu, Y. / Ye, S. / Zhang, R.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Characterization by high-resolution crystal structure analysis of a triple-helix region of human collagen type III with potent cell adhesion activity.
Authors: Hua, C. / Zhu, Y. / Xu, W. / Ye, S. / Zhang, R. / Lu, L. / Jiang, S.
History
DepositionJun 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: collagen type III peptide
B: collagen type III peptide
C: collagen type III peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3865
Polymers8,2323
Non-polymers1542
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-26 kcal/mol
Surface area5700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.835, 14.133, 57.920
Angle α, β, γ (deg.)90.00, 101.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide collagen type III peptide


Mass: 2743.960 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.89 Å3/Da / Density % sol: 35.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 400, 0.1M Na Acetate pH 4.6, 0.1M Cadmium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979304897 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979304897 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 10258 / % possible obs: 98.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.21
Reflection shellResolution: 1.5→1.52 Å / Rmerge(I) obs: 0.11 / Num. unique obs: 469

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WUH

2wuh


Resolution: 1.501→18.911 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1952 523 5.1 %
Rwork0.1726 --
obs0.1738 10246 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.501→18.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms577 0 10 115 702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006631
X-RAY DIFFRACTIONf_angle_d1.458874
X-RAY DIFFRACTIONf_dihedral_angle_d8.84377
X-RAY DIFFRACTIONf_chiral_restr0.10480
X-RAY DIFFRACTIONf_plane_restr0.007120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5011-1.6520.23391360.20192377X-RAY DIFFRACTION99
1.652-1.89090.24761310.20062418X-RAY DIFFRACTION99
1.8909-2.38160.21651220.1742444X-RAY DIFFRACTION98
2.3816-18.91280.16311340.15812484X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.492-3.17862.41833.3482-0.64246.9379-0.0846-0.8227-0.66690.01810.288-0.14690.6258-0.289-0.30380.1602-0.01710.0180.33570.04060.191729.80954.008436.2991
21.3776-0.01552.1031-0.0585-0.22112.5064-0.2558-0.23870.24770.0975-0.06930.0483-0.4218-0.28940.16450.16510.0082-0.03320.1108-0.01810.08684.61862.417711.3654
32.4831-3.21381.43465.4977-1.7550.8759-0.30150.47880.5006-1.0433-0.37911.6854-0.3816-0.96030.21210.16460.0379-0.18350.3871-0.08450.5297-18.5706-1.3302-9.1481
41.69641.26811.81584.35682.27222.2034-0.4344-0.071.05860.4818-0.0311-0.8571-0.18920.55470.35780.2969-0.0797-0.09460.3911-0.07340.35132.07428.09937.1656
58.89972.02318.72121.79742.15879.6424-0.16750.36680.04620.05580.2384-0.1497-0.29410.61930.05010.1642-0.00560.0150.17-0.02680.121213.43951.982118.1993
62.2237-0.41692.03360.58960.12082.36660.0044-0.317-0.0311-0.0063-0.04550.09010.3555-0.74880.02220.1224-0.01740.01930.1624-0.0010.1191-5.5944-1.7695.1505
78.6463-0.53176.52171.6999-0.18794.9448-0.2995-0.38090.35710.0023-0.12140.1458-0.2605-0.76110.410.1340.0229-0.01180.1973-0.04960.1995-14.48122.6616-5.7489
82.23492.02552.09147.83494.53473.1091-0.07580.09910.12910.20210.15590.009-0.40320.96070.01950.2189-0.05350.01970.5759-0.00870.248336.66027.678535.7719
92.0893.50810.85725.95472.01338.66610.281-0.239-0.9420.1739-0.1934-0.43090.46310.8718-0.27480.2601-0.036-0.09760.16320.03660.237919.05760.677426.6437
108.591-1.73516.40821.2218-1.33274.4715-0.3975-0.49730.20.27650.09540.0169-0.2515-0.360.31110.1270.0375-0.00280.1263-0.01670.10860.55672.255311.6968
113.4704-0.70234.58938.00530.74987.22080.25980.08590.2164-0.3481-0.71040.4205-0.028-0.28570.19730.09940.0745-0.00910.1487-0.08640.1568-11.27120.9533-8.9867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 30 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 7 )
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 18 )
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 24 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 28 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 7 )
9X-RAY DIFFRACTION9chain 'C' and (resid 9 through 13 )
10X-RAY DIFFRACTION10chain 'C' and (resid 14 through 24 )
11X-RAY DIFFRACTION11chain 'C' and (resid 25 through 30 )

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