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- PDB-1o91: Crystal Structure of a Collagen VIII NC1 Domain Trimer -

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Basic information

Entry
Database: PDB / ID: 1o91
TitleCrystal Structure of a Collagen VIII NC1 Domain Trimer
ComponentsCOLLAGEN ALPHA 1(VIII) CHAIN
KeywordsSTRUCTURAL PROTEIN / COLLAGEN / C1Q_LIKE_DOMAIN / EXTRACELLULAR MATRIX / ADHESION / CONNECTIVE TISSUE
Function / homology
Function and homology information


Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / Integrin cell surface interactions / camera-type eye morphogenesis / collagen trimer / positive regulation of cell-substrate adhesion / extracellular matrix structural constituent / endodermal cell differentiation ...Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / Integrin cell surface interactions / camera-type eye morphogenesis / collagen trimer / positive regulation of cell-substrate adhesion / extracellular matrix structural constituent / endodermal cell differentiation / basement membrane / extracellular matrix organization / extracellular matrix / epithelial cell proliferation / angiogenesis / collagen-containing extracellular matrix / cell adhesion / extracellular space
Similarity search - Function
C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Collagen alpha-1(VIII) chain
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKvansakul, M. / Bogin, O. / Hohenester, E. / Yayon, A.
Citation
Journal: Matrix Biol. / Year: 2003
Title: Crystal Structure of the Collagen Alpha1(Viii) Nc1 Trimer.
Authors: Kvansakul, M. / Bogin, O. / Hohenester, E. / Yayon, A.
#1: Journal: Structure / Year: 2002
Title: Insight Into Schmid Metaphyseal Chondrodysplasia from the Crystal Structure of the Collagen X Nc1 Domain Trimer.
Authors: Bogin, O. / Kvansakul, M. / Rom, E. / Singer, J. / Yayon, A. / Hohenester, E.
#2: Journal: Int. J. Biochem. Cell Biol. / Year: 1997
Title: Type Viii Collagen
Authors: Shuttleworth, C.A.
History
DepositionDec 10, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2003Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLLAGEN ALPHA 1(VIII) CHAIN
B: COLLAGEN ALPHA 1(VIII) CHAIN
C: COLLAGEN ALPHA 1(VIII) CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9145
Polymers59,2033
Non-polymers7112
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-61.6 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.590, 82.550, 89.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.19881, 0.26493, -0.94355), (0.9734, 0.05852, 0.22153), (0.11391, -0.96249, -0.24624)34.44011, -6.45202, 48.04818
2given(0.19517, 0.97545, 0.10203), (0.26909, 0.04678, -0.96198), (-0.94313, 0.21521, -0.25335)-5.70255, 37.41146, 46.00101

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Components

#1: Protein COLLAGEN ALPHA 1(VIII) CHAIN


Mass: 19734.426 Da / Num. of mol.: 3 / Fragment: NONHELICAL REGION (NC1), RESIDUES 613-743
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: P89BLUESCRIPT / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q00780
#2: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.1 Å3/Da / Density % sol: 43 %
Crystal growpH: 7.5
Details: 1.7 M AMMONIUM SULFATE, 4 % (V/V)ISOPROPANOL, pH 7.50
Crystal grow
*PLUS
pH: 9.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
20.1 Mglycine-NaOH1droppH9.5
30.1 M1dropKCl
40.05 %CHAPS1drop
51.7-2.0 Mammonium sulfate1reservoir
64 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 2002 / Details: OSMIC MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 37444 / % possible obs: 98.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.7
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.7 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. obs: 37514 / Redundancy: 5.6 % / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 98.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.24

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GR3

1gr3


Resolution: 1.9→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: INDIVIDUALLY RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3756 9.9 %RANDOM
Rwork0.185 ---
obs0.185 37444 98.7 %-
Solvent computationSolvent model: FLAT / Bsol: 68 Å2 / ksol: 0.4 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 37 268 3425
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.5
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_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.62.5
LS refinement shellResolution: 1.9→1.91 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.247 67 10.5 %
Rwork0.21 641 -
obs--100 %
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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