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- PDB-1xdd: X-ray structure of LFA-1 I-domain in complex with LFA703 at 2.2A ... -

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Basic information

Entry
Database: PDB / ID: 1xdd
TitleX-ray structure of LFA-1 I-domain in complex with LFA703 at 2.2A resolution
ComponentsIntegrin alpha-L
KeywordsIMMUNE SYSTEM / Rossmann fold / I-domain
Function / homology
Function and homology information


memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / receptor clustering ...memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / receptor clustering / Integrin cell surface interactions / phagocytosis / specific granule membrane / cell adhesion molecule binding / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell adhesion / inflammatory response / external side of plasma membrane / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / metal ion binding / membrane / plasma membrane
Similarity search - Function
Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / 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. ...Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / 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
Chem-AAY / Integrin alpha-L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWeitz-Schmidt, G. / Welzenbach, K. / Dawson, J. / Kallen, J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Improved lymphocyte function-associated antigen-1 (LFA-1) inhibition by statin derivatives: molecular basis determined by x-ray analysis and monitoring of LFA-1 conformational changes in vitro and ex vivo
Authors: Weitz-Schmidt, G. / Welzenbach, K. / Dawson, J. / Kallen, J.
History
DepositionSep 6, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 20, 2013Group: Database references
Revision 1.4Nov 12, 2014Group: Structure summary
Revision 1.5Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-L
B: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1076
Polymers42,8512
Non-polymers1,2564
Water4,990277
1
A: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0543
Polymers21,4261
Non-polymers6282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0543
Polymers21,4261
Non-polymers6282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.700, 116.700, 82.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-576-

HOH

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Components

#1: Protein Integrin alpha-L / Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function associated molecule ...Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function associated molecule 1 / alpha chain / CD11a / alphaLbeta2 / CD11a/CD18


Mass: 21425.561 Da / Num. of mol.: 2 / Fragment: I-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: P20701
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AAY / 8-[2-((2S)-4-HYDROXY-1-{[5-(HYDROXYMETHYL)-6-METHOXY-2-NAPHTHYL]METHYL}-6-OXOPIPERIDIN-2-YL)ETHYL]-3,7-DIMETHYL-1,2,3,7,8,8A-HEXAHYDRONAPHTHALEN-1-YL 2-METHYLBUTANOATE / LFA703


Mass: 603.788 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H49NO6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE IS TRP ACCORDING TO LARSON R.S. ET AL. [J. CELL BIOL. 108:703-712(1989)] OR LOFTUS B.J. ...THE RESIDUE IS TRP ACCORDING TO LARSON R.S. ET AL. [J. CELL BIOL. 108:703-712(1989)] OR LOFTUS B.J. ET AL. [GENOMICS 60:295-308(1999)].

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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: 3.5 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium acetate, sodium acetate, glycerol, PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.80074 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.80074 Å / Relative weight: 1
ReflectionResolution: 2.2→8 Å / Num. all: 28795 / Num. obs: 28795 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rsym value: 0.094 / Net I/σ(I): 22.7
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 7.8 / Rsym value: 0.286 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CQP

1cqp


Resolution: 2.2→8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.966 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20643 1464 5.1 %RANDOM
Rwork0.16138 ---
obs0.16368 27286 99.71 %-
all-27286 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.967 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2936 0 90 277 3303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223132
X-RAY DIFFRACTIONr_bond_other_d0.0010.022836
X-RAY DIFFRACTIONr_angle_refined_deg1.5122.0014236
X-RAY DIFFRACTIONr_angle_other_deg0.84336640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7065360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76425.294136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33315562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.82156
X-RAY DIFFRACTIONr_chiral_restr0.0950.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02628
X-RAY DIFFRACTIONr_nbd_refined0.2090.2547
X-RAY DIFFRACTIONr_nbd_other0.1840.22644
X-RAY DIFFRACTIONr_nbtor_other0.0910.21680
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2212
X-RAY DIFFRACTIONr_metal_ion_refined0.0750.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1760.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.214
X-RAY DIFFRACTIONr_mcbond_it1.5811.52322
X-RAY DIFFRACTIONr_mcbond_other0.2651.5740
X-RAY DIFFRACTIONr_mcangle_it1.84722936
X-RAY DIFFRACTIONr_scbond_it2.85531639
X-RAY DIFFRACTIONr_scangle_it4.1254.51298
LS refinement shellResolution: 2.201→2.254 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.273 95
Rwork0.182 1860

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