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- PDB-2uur: N-terminal NC4 domain of collagen IX -

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Basic information

Entry
Database: PDB / ID: 2uur
TitleN-terminal NC4 domain of collagen IX
ComponentsCOLLAGEN ALPHA-1(IX) CHAIN
KeywordsSTRUCTURAL PROTEIN / GLYCOPROTEIN / HYDROXYLATION / NC4 / COLLAGEN / COLLAGEN IX / POLYMORPHISM / EXTRACELLULAR MATRIX / ALTERNATIVE SPLICING
Function / homology
Function and homology information


collagen type IX trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / NCAM1 interactions / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / ECM proteoglycans / Integrin cell surface interactions ...collagen type IX trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / NCAM1 interactions / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / ECM proteoglycans / Integrin cell surface interactions / extracellular matrix organization / animal organ morphogenesis / carbohydrate binding / collagen-containing extracellular matrix / endoplasmic reticulum lumen / protein homodimerization activity / extracellular space / extracellular region / metal ion binding
Similarity search - Function
: / Thrombospondin N-terminal -like domains. / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Collagen alpha-1(IX) chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsLeppanen, V.-M. / Tossavainen, H. / Permi, P. / Lehtio, L. / Ronnholm, G. / Goldman, A. / Kilpelainen, I. / Pihlajamaa, T.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure of the N-Terminal Nc4 Domain of Collagen Ix, a Zinc Binding Member of the Laminin-Neurexin-Sex Hormone Binding Globulin (Lns) Domain Family.
Authors: Leppanen, V.-M. / Tossavainen, H. / Permi, P. / Lehtio, L. / Ronnholm, G. / Goldman, A. / Kilpelainen, I. / Pihlajamaa, T.
History
DepositionMar 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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

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Assembly

Deposited unit
A: COLLAGEN ALPHA-1(IX) CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9558
Polymers27,4831
Non-polymers4727
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.888, 81.888, 71.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein COLLAGEN ALPHA-1(IX) CHAIN / IX CHAIN / COLLAGEN IX ALPHA1 CHAIN


Mass: 27483.232 Da / Num. of mol.: 1 / Fragment: NC4 DOMAIN, RESIDUES 24-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA DE3 / References: UniProt: P20849
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE GENBANK ENTRY INCLUDES A SIGNAL PEPTIDE OF 23 RESIDUES, WHICH IS OMITTED FROM THE STUDIED MACROMOLECULE

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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: 2.2 Å3/Da / Density % sol: 42 %
Crystal growpH: 6.5 / Details: 100 MM MES, PH 6.5 10 MM ZNSO4 20% MME-PEG 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9797, 0.9796, 0.8856
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 20, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97961
30.88561
ReflectionResolution: 1.8→20 Å / Num. obs: 21918 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.5
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2639988.95 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1069 4.9 %RANDOM
Rwork0.188 ---
obs0.188 21918 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.4928 Å2 / ksol: 0.35623 e/Å3
Displacement parametersBiso mean: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.79 Å20 Å20 Å2
2--4.79 Å20 Å2
3----9.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 0 26 209 1892
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_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 174 4.8 %
Rwork0.259 3452 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMEDO_CNS_TOP.TXT
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4EDO_CNS_PAR.TXTWATER.TOP

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