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- PDB-1n3y: Crystal structure of the alpha-X beta2 integrin I domain -

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Basic information

Entry
Database: PDB / ID: 1n3y
TitleCrystal structure of the alpha-X beta2 integrin I domain
ComponentsIntegrin alpha-X
KeywordsCELL ADHESION / alpha/beta Rossmann fold
Function / homology
Function and homology information


positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / positive regulation of myelination / heterotypic cell-cell adhesion / integrin complex / cell adhesion mediated by integrin / tertiary granule membrane / ficolin-1-rich granule membrane / ECM proteoglycans / Integrin cell surface interactions ...positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / positive regulation of myelination / heterotypic cell-cell adhesion / integrin complex / cell adhesion mediated by integrin / tertiary granule membrane / ficolin-1-rich granule membrane / ECM proteoglycans / Integrin cell surface interactions / cell-matrix adhesion / secretory granule membrane / integrin-mediated signaling pathway / animal organ morphogenesis / Cell surface interactions at the vascular wall / receptor tyrosine kinase binding / cell-cell adhesion / positive regulation of angiogenesis / integrin binding / signaling receptor activity / Interleukin-4 and Interleukin-13 signaling / defense response to virus / cell adhesion / positive regulation of cell migration / external side of plasma membrane / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / cell surface / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : ...: / Integrin alpha-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsVorup-Jensen, T. / Ostermeier, C. / Shimaoka, M. / Hommel, U. / Springer, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structure and allosteric regulation of the alpha X beta 2 integrin I domain.
Authors: Vorup-Jensen, T. / Ostermeier, C. / Shimaoka, M. / Hommel, U. / Springer, T.A.
History
DepositionOct 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrin alpha-X


Theoretical massNumber of molelcules
Total (without water)22,3551
Polymers22,3551
Non-polymers00
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.694, 84.694, 65.776
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Integrin alpha-X / Leukocyte adhesion glycoprotein p150 / 95 alpha chain / Leukocyte adhesion receptor p150 / 95 / CD11c / Leu M5


Mass: 22355.283 Da / Num. of mol.: 1 / Fragment: I domain / Mutation: T192S, T234A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAX OR CD11C / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20702
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.7 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulfate, glycerol, sodium acetate, EDTA, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 mMHEPES1droppH7.0
32.2-2.6 Mammonium sulfate1reservoir
417.5 %glycerol1reservoiror 20%
5100 mMsodium acetate1reservoirpH5.0
65 mMEDTA1reservoiror 15mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.54178 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 18, 2001 / Details: osmic mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 32357 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.9
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.229 / Num. unique all: 3199 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 32389 / Num. measured all: 278307
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNX2000.1refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house structure of a Mac1 I domain

Resolution: 1.65→27.72 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1601 5 %RANDOM
Rwork0.208 ---
all0.209 32357 --
obs0.209 32311 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.5352 Å2 / ksol: 0.412969 e/Å3
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å2-0.74 Å20 Å2
2---2.05 Å20 Å2
3---4.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→27.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 0 291 1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.452.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 283 5.3 %
Rwork0.269 5055 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
% reflection Rfree: 2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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