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- PDB-7wws: Structure of a triple-helix region of human collagen type III fro... -

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Basic information

Entry
Database: PDB / ID: 7wws
TitleStructure of a triple-helix region of human collagen type III from Trautec
ComponentsCollagen alpha-1(III) chain
KeywordsSTRUCTURAL PROTEIN / Human collagen type III Triple-helix region Crystal structure Integrin recognition motif
Function / homology
Function and homology information


collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / transforming growth factor beta1 production / elastic fiber assembly / negative regulation of neuron migration / Collagen chain trimerization / platelet-derived growth factor binding / endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength ...collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / transforming growth factor beta1 production / elastic fiber assembly / negative regulation of neuron migration / Collagen chain trimerization / platelet-derived growth factor binding / endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / Extracellular matrix organization / basement membrane organization / layer formation in cerebral cortex / Collagen biosynthesis and modifying enzymes / peptide cross-linking / tissue homeostasis / Signaling by PDGF / negative regulation of immune response / digestive tract development / NCAM1 interactions / response to angiotensin / collagen fibril organization / Scavenging by Class A Receptors / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / Syndecan interactions / positive regulation of Rho protein signal transduction / skin development / SMAD binding / Collagen degradation / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / chondrocyte differentiation / supramolecular fiber organization / cell-matrix adhesion / extracellular matrix organization / transforming growth factor beta receptor signaling pathway / response to cytokine / integrin-mediated signaling pathway / cellular response to amino acid stimulus / lung development / neuron migration / wound healing / response to radiation / multicellular organism growth / platelet activation / cerebral cortex development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / heart development / fibroblast proliferation / protease binding / collagen-containing extracellular matrix / in utero embryonic development / endoplasmic reticulum lumen / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
Collagen alpha-1(III) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsQian, S. / Li, H. / Fan, X. / Tian, X. / Li, J. / Wang, L. / Chu, Y.
CitationJournal: To Be Published
Title: Structure of a triple-helix region of human collagen type III from Trautec
Authors: Qian, S. / Li, H. / Fan, X. / Tian, X. / Li, J. / Wang, L. / Chu, Y.
History
DepositionFeb 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Derived calculations / Structure summary
Category: atom_type / citation / struct
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.title / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagen alpha-1(III) chain
B: Collagen alpha-1(III) chain
C: Collagen alpha-1(III) chain


Theoretical massNumber of molelcules
Total (without water)7,3943
Polymers7,3943
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-18 kcal/mol
Surface area5030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)18.582, 19.320, 74.234
Angle α, β, γ (deg.)90.000, 96.886, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Collagen alpha-1(III) chain


Mass: 2464.582 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02461
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.79 Å3/Da / Density % sol: 31.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgAc2, 0.1M Na cacodylate pH6.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.3→36.85 Å / Num. obs: 13244 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 58.8
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.041 / Num. unique obs: 658

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2cuo

2cuo


Resolution: 1.3→24.578 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.209 / SU ML: 0.024 / Cross valid method: FREE R-VALUE / ESU R: 0.049 / ESU R Free: 0.049
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1582 629 4.752 %
Rwork0.1144 12607 -
all0.116 --
obs-13236 99.887 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.945 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.299 Å2
2---0.012 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.3→24.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms522 0 0 156 678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.012559
X-RAY DIFFRACTIONr_bond_other_d0.0020.016456
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.751793
X-RAY DIFFRACTIONr_angle_other_deg1.1991.5511122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.872580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.8532012
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5251528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.07153
X-RAY DIFFRACTIONr_chiral_restr0.0840.273
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02655
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0267
X-RAY DIFFRACTIONr_nbd_refined0.2320.2198
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.2403
X-RAY DIFFRACTIONr_nbtor_refined0.170.2308
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.2211
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.288
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.216
X-RAY DIFFRACTIONr_nbd_other0.2510.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3660.248
X-RAY DIFFRACTIONr_mcbond_it2.2581.128323
X-RAY DIFFRACTIONr_mcbond_other2.2641.13321
X-RAY DIFFRACTIONr_mcangle_it2.4371.679399
X-RAY DIFFRACTIONr_mcangle_other2.4361.678399
X-RAY DIFFRACTIONr_scbond_it2.9631.429236
X-RAY DIFFRACTIONr_scbond_other2.9371.428236
X-RAY DIFFRACTIONr_scangle_it3.5592.065393
X-RAY DIFFRACTIONr_scangle_other3.552.064393
X-RAY DIFFRACTIONr_lrange_it4.24918.979703
X-RAY DIFFRACTIONr_lrange_other4.05117.96659
X-RAY DIFFRACTIONr_rigid_bond_restr8.07631015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.3340.145560.091914X-RAY DIFFRACTION100
1.334-1.370.172470.094886X-RAY DIFFRACTION100
1.37-1.410.143470.109880X-RAY DIFFRACTION99.8922
1.41-1.4530.145360.095846X-RAY DIFFRACTION99.8867
1.453-1.5010.162420.106821X-RAY DIFFRACTION100
1.501-1.5540.166410.104807X-RAY DIFFRACTION99.8822
1.554-1.6120.145370.096762X-RAY DIFFRACTION100
1.612-1.6780.123400.1758X-RAY DIFFRACTION100
1.678-1.7530.113300.1709X-RAY DIFFRACTION100
1.753-1.8380.16300.099669X-RAY DIFFRACTION99.5726
1.838-1.9380.179350.103661X-RAY DIFFRACTION99.7135
1.938-2.0550.142360.104611X-RAY DIFFRACTION99.8457
2.055-2.1970.183340.104576X-RAY DIFFRACTION99.8363
2.197-2.3730.141340.113536X-RAY DIFFRACTION100
2.373-2.5990.193190.121492X-RAY DIFFRACTION100
2.599-2.9050.097200.118464X-RAY DIFFRACTION99.7938
2.905-3.3540.16100.132426X-RAY DIFFRACTION99.7712
3.354-4.1050.14140.122338X-RAY DIFFRACTION99.7167
4.105-5.7970.125100.149288X-RAY DIFFRACTION100
5.797-24.5780.518110.282163X-RAY DIFFRACTION99.4286

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