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- PDB-1ck4: CRYSTAL STRUCTURE OF RAT A1B1 INTEGRIN I-DOMAIN. -

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Basic information

Entry
Database: PDB / ID: 1ck4
TitleCRYSTAL STRUCTURE OF RAT A1B1 INTEGRIN I-DOMAIN.
ComponentsINTEGRIN ALPHA-1
KeywordsSTRUCTURAL PROTEIN / I-DOMAIN / METAL BINDING / COLLAGEN / ADHESION
Function / homology
Function and homology information


Integrin cell surface interactions / Smooth Muscle Contraction / cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / basal part of cell / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / : ...Integrin cell surface interactions / Smooth Muscle Contraction / cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / basal part of cell / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / : / collagen binding / neutrophil chemotaxis / cell-matrix adhesion / acrosomal vesicle / neuron projection morphogenesis / cell chemotaxis / integrin-mediated signaling pathway / cell-cell adhesion / vasodilation / positive regulation of neuron apoptotic process / integrin binding / protein phosphatase binding / perikaryon / positive regulation of MAPK cascade / cell adhesion / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / focal adhesion / cell surface / metal ion binding
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / 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 ...: / Integrin alpha Ig-like domain 3 / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNolte, M. / Pepinsky, R.B. / Venyaminov, S.Y. / Koteliansky, V. / Gotwals, P.J. / Karpusas, M.
CitationJournal: FEBS Lett. / Year: 1999
Title: Crystal structure of the alpha1beta1 integrin I-domain: insights into integrin I-domain function.
Authors: Nolte, M. / Pepinsky, R.B. / Venyaminov, S.Y.u. / Koteliansky, V. / Gotwals, P.J. / Karpusas, M.
History
DepositionApr 27, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTEGRIN ALPHA-1
B: INTEGRIN ALPHA-1


Theoretical massNumber of molelcules
Total (without water)44,2362
Polymers44,2362
Non-polymers00
Water3,873215
1
A: INTEGRIN ALPHA-1


Theoretical massNumber of molelcules
Total (without water)22,1181
Polymers22,1181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: INTEGRIN ALPHA-1


Theoretical massNumber of molelcules
Total (without water)22,1181
Polymers22,1181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.770, 85.920, 132.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99929, 0.00081, 0.03763), (0.03596, 0.27445, -0.96093), (-0.01111, 0.9616, 0.27422)
Vector: -7.52793, 41.65117, -46.95238)

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Components

#1: Protein INTEGRIN ALPHA-1


Mass: 22118.053 Da / Num. of mol.: 2 / Fragment: I-DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): DH5A / Production host: Escherichia coli (E. coli) / References: UniProt: P18614
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 4.22 Å3/Da / Density % sol: 45.03 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMTris1drop
210 mM2-mercaptoethanol1drop
311 mg/mlprotein1drop
425 %(w/v)PEG80001reservoir
50.1 Msodium cacodylate1reservoir
60.2 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 19238 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 12 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / % possible obs: 77.6 % / Mean I/σ(I) obs: 3.14

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AOX

1aox


Resolution: 2.2→100 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: FOR CHAIN A, SIDE CHAINS OF RESIDUES 145, 146, 234 ARE ASSIGNED 0.0 OCCUPANCY DUE TO ABSENCE OF ELECTRON DENSITY FOR THE SIDE CHAINS. FOR CHAIN B, SIDE CHAINS OF RESIDUES 145, 175, 234 ARE ...Details: FOR CHAIN A, SIDE CHAINS OF RESIDUES 145, 146, 234 ARE ASSIGNED 0.0 OCCUPANCY DUE TO ABSENCE OF ELECTRON DENSITY FOR THE SIDE CHAINS. FOR CHAIN B, SIDE CHAINS OF RESIDUES 145, 175, 234 ARE ASSIGNED 0.0 OCCUPANCY DUE TO ABSENCE OF ELECTRON DENSITY FOR THE SIDE CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.299 -10 %RANDOM
Rwork0.234 ---
obs-19238 91.3 %-
Refinement stepCycle: LAST / Resolution: 2.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3753 0 0 215 3968
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.6

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