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- PDB-1ij9: Highly Hydrated Human VCAM-1 Fragment -

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Basic information

Entry
Database: PDB / ID: 1ij9
TitleHighly Hydrated Human VCAM-1 Fragment
ComponentsVASCULAR CELL ADHESION PROTEIN 1
KeywordsCELL ADHESION / integrin solvation
Function / homology
Function and homology information


cardiac neuron differentiation / alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex / cell adhesion mediator activity / cell-cell adhesion in response to extracellular stimulus / chronic inflammatory response / membrane to membrane docking / leukocyte tethering or rolling / innervation / primary methylamine oxidase activity / amine metabolic process ...cardiac neuron differentiation / alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex / cell adhesion mediator activity / cell-cell adhesion in response to extracellular stimulus / chronic inflammatory response / membrane to membrane docking / leukocyte tethering or rolling / innervation / primary methylamine oxidase activity / amine metabolic process / podosome / heterotypic cell-cell adhesion / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / response to ionizing radiation / response to zinc ion / microvillus / : / cellular response to vascular endothelial growth factor stimulus / Integrin cell surface interactions / positive regulation of T cell proliferation / cell adhesion molecule binding / B cell differentiation / response to nutrient / cell-matrix adhesion / cell chemotaxis / filopodium / response to nicotine / sarcolemma / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / integrin binding / apical part of cell / cellular response to tumor necrosis factor / Interleukin-4 and Interleukin-13 signaling / response to ethanol / response to lipopolysaccharide / early endosome / cell adhesion / response to hypoxia / inflammatory response / external side of plasma membrane / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / plasma membrane
Similarity search - Function
Vascular cell adhesion molecule-1 / : / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain ...Vascular cell adhesion molecule-1 / : / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / 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
Vascular cell adhesion protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTaylor, P. / Bilsland, M. / Walkinshaw, M.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: A new conformation of the integrin-binding fragment of human VCAM-1 crystallizes in a highly hydrated packing arrangement.
Authors: Taylor, P. / Bilsland, M. / Walkinshaw, M.D.
History
DepositionApr 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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: VASCULAR CELL ADHESION PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)21,8941
Polymers21,8941
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.939, 152.939, 45.976
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein VASCULAR CELL ADHESION PROTEIN 1 / VCAM-1


Mass: 21893.834 Da / Num. of mol.: 1 / Fragment: VCAM-D1,D2 (INTEGRIN BINDING FRAGMENT)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P19320
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 7.09 Å3/Da / Density % sol: 82.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes, Tris, Ammonium Sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMHEPES1drop
350 mMTris1reservoir
442 %(v/v)satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 11, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
21.54181
ReflectionResolution: 3→24 Å / Num. all: 183518 / Num. obs: 183518 / % possible obs: 99.9 % / Redundancy: 9.44 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 19.59
Reflection shellResolution: 3→3.05 Å / Redundancy: 9.26 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 5.14 / % possible all: 100
Reflection
*PLUS
Num. obs: 12530 / Num. measured all: 183518
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 622 / Num. measured obs: 5762

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vca

1vca


Resolution: 3→24 Å / Cross valid method: FREE R / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.238 1293 RANDOM
Rwork0.208 --
all0.208 12530 -
obs0.208 12530 -
Refinement stepCycle: LAST / Resolution: 3→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1533 0 0 50 1583
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.311
X-RAY DIFFRACTIONx_dihedral_angle_d28.713
X-RAY DIFFRACTIONx_improper_angle_d1.058
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.713
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.058

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