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- PDB-5nir: Crystal structure of collagen 2A vWC domain -

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Basic information

Entry
Database: PDB / ID: 5nir
TitleCrystal structure of collagen 2A vWC domain
ComponentsCollagen alpha-1(II) chain
KeywordsSTRUCTURAL PROTEIN / collagen / vwc / ECM / BMP-2
Function / homology
Function and homology information


collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / Extracellular matrix organization ...collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / Extracellular matrix organization / notochord development / limb bud formation / Collagen biosynthesis and modifying enzymes / cartilage development involved in endochondral bone morphogenesis / tissue homeostasis / MHC class II protein binding / Signaling by PDGF / cellular response to BMP stimulus / endochondral ossification / NCAM1 interactions / collagen fibril organization / cartilage development / proteoglycan binding / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / inner ear morphogenesis / cartilage condensation / roof of mouth development / Collagen degradation / Non-integrin membrane-ECM interactions / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ECM proteoglycans / Integrin cell surface interactions / chondrocyte differentiation / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / central nervous system development / skeletal system development / sensory perception of sound / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of gene expression / collagen-containing extracellular matrix / endoplasmic reticulum lumen / protein homodimerization activity / 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 / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Collagen alpha-1(II) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å
AuthorsFischer, G. / Blythe, E. / Hyvonen, M.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural analyses of von Willebrand factor C domains of collagen 2A and CCN3 reveal an alternative mode of binding to bone morphogenetic protein-2.
Authors: Xu, E.R. / Blythe, E.E. / Fischer, G. / Hyvonen, M.
History
DepositionMar 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagen alpha-1(II) chain
B: Collagen alpha-1(II) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,57524
Polymers15,8442
Non-polymers2,73122
Water28816
1
A: Collagen alpha-1(II) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,15113
Polymers7,9221
Non-polymers1,22912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Collagen alpha-1(II) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,42411
Polymers7,9221
Non-polymers1,50210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.930, 60.160, 86.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Collagen alpha-1(II) chain / Alpha-1 type II collagen


Mass: 7921.925 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL2A1 / Plasmid: pHAT3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02458

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Non-polymers , 5 types, 38 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL, PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, pH 7.5, 40% PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.74→49.37 Å / Num. obs: 17667 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 30.54 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 22.7
Reflection shellResolution: 1.744→1.75 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.709 / % possible all: 100

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Processing

Software
NameVersionClassification
AutoPROCdata reduction
XDS(VERSION September 2data reduction
Aimlessdata scaling
BUSTER2.10.3refinement
autoSHARPphasing
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.74→49.37 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.231 894 5.07 %RANDOM
Rwork0.209 ---
obs0.21 17616 99.2 %-
Displacement parametersBiso mean: 39.26 Å2
Baniso -1Baniso -2Baniso -3
1--5.5435 Å20 Å20 Å2
2--2.6156 Å20 Å2
3---2.9278 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.74→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms993 0 181 16 1190
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011223HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.221591HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d478SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes33HARMONIC2
X-RAY DIFFRACTIONt_gen_planes147HARMONIC5
X-RAY DIFFRACTIONt_it1223HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.94
X-RAY DIFFRACTIONt_other_torsion14.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion147SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1435SEMIHARMONIC4
LS refinement shellResolution: 1.74→1.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.257 140 5.22 %
Rwork0.222 2540 -
all0.224 2680 -
obs--95.15 %

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