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- PDB-3qr2: Wild type CD147 Ig0 domain -

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Basic information

Entry
Database: PDB / ID: 3qr2
TitleWild type CD147 Ig0 domain
ComponentsBasigin
KeywordsCELL ADHESION / CD147 / EMMPRIN / Immunoglobulin-like domain / beta sheet / Structural Genomics / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / endothelial tube morphogenesis / neural retina development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / endothelial tube morphogenesis / neural retina development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / D-mannose binding / decidualization / positive regulation of vascular endothelial growth factor production / photoreceptor outer segment / Integrin cell surface interactions / response to cAMP / neutrophil chemotaxis / embryo implantation / Degradation of the extracellular matrix / photoreceptor inner segment / positive regulation of endothelial cell migration / protein localization to plasma membrane / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / melanosome / signaling receptor activity / virus receptor activity / basolateral plasma membrane / angiogenesis / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / endoplasmic reticulum membrane / mitochondrion / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsRedzic, J.S. / Armstrong, G.S. / Isern, N.G. / Kieft, J.S. / Eisenmesser, E.Z. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Retinal Specific CD147 Ig0 Domain: From Molecular Structure to Biological Activity.
Authors: Redzic, J.S. / Armstrong, G.S. / Isern, N.G. / Jones, D.N. / Kieft, J.S. / Eisenmesser, E.Z.
History
DepositionFeb 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Basigin
B: Basigin


Theoretical massNumber of molelcules
Total (without water)30,6022
Polymers30,6022
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-8 kcal/mol
Surface area12610 Å2
MethodPISA
2
A: Basigin
B: Basigin

A: Basigin
B: Basigin


Theoretical massNumber of molelcules
Total (without water)61,2044
Polymers61,2044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area5310 Å2
ΔGint-25 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.257, 80.257, 160.674
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody Basigin / 5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / EMMPRIN / ...5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / EMMPRIN / Leukocyte activation antigen M6 / OK blood group antigen / Tumor cell-derived collagenase stimulatory factor / TCSF


Mass: 15300.972 Da / Num. of mol.: 2 / Fragment: UNP residues 23-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BSG, UNQ6505/PRO21383 / Production host: Escherichia coli (E. coli) / References: UniProt: P35613
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAS PER AUTHORS ILE IS THE CORRECT RESIDUE AT POSITION 45

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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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 Na2SO4, 20% w/v PEG sulfate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.2053 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 4, 2010
RadiationMonochromator: Rosenbaum-Rock double Si111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2053 Å / Relative weight: 1
ReflectionResolution: 2.3→42.42 Å / Num. obs: 14268 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine:1.6.4_486)model building
PHENIX(phenix.refine: 1.6.4_486)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementResolution: 2.3→42.42 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 29.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3073 1421 9.99 %
Rwork0.2643 --
obs0.2686 14231 99.66 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.716 Å2 / ksol: 0.281 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7305 Å20 Å20 Å2
2---0.7305 Å20 Å2
3---1.4611 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 0 98 1930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081884
X-RAY DIFFRACTIONf_angle_d1.0982574
X-RAY DIFFRACTIONf_dihedral_angle_d16.693660
X-RAY DIFFRACTIONf_chiral_restr0.074278
X-RAY DIFFRACTIONf_plane_restr0.004340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.31271350.25091231X-RAY DIFFRACTION99
2.3822-2.47760.34791380.26721236X-RAY DIFFRACTION100
2.4776-2.59030.34851400.29371267X-RAY DIFFRACTION100
2.5903-2.72690.34131370.29231238X-RAY DIFFRACTION99
2.7269-2.89770.31271410.27211264X-RAY DIFFRACTION100
2.8977-3.12130.32261390.26681261X-RAY DIFFRACTION100
3.1213-3.43530.29371410.27191276X-RAY DIFFRACTION100
3.4353-3.93210.35771450.30381291X-RAY DIFFRACTION100
3.9321-4.95280.23751450.20331316X-RAY DIFFRACTION100
4.9528-42.420.30211600.2731430X-RAY DIFFRACTION100

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