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- PDB-1xdg: X-ray structure of LFA-1 I-domain in complex with LFA878 at 2.1A ... -

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Basic information

Entry
Database: PDB / ID: 1xdg
TitleX-ray structure of LFA-1 I-domain in complex with LFA878 at 2.1A resolution
ComponentsIntegrin alpha-L
KeywordsIMMUNE SYSTEM / Rossman-fold / I-domain
Function / homology
Function and homology information


memory T cell extravasation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / receptor clustering ...memory T cell extravasation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / receptor clustering / Integrin cell surface interactions / specific granule membrane / phagocytosis / 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 / membrane / metal ion binding / 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 Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / 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 Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / 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-AB8 / Integrin alpha-L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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)44,0936
Polymers42,8512
Non-polymers1,2424
Water2,666148
1
A: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0473
Polymers21,4261
Non-polymers6212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0473
Polymers21,4261
Non-polymers6212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.900, 77.400, 92.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-AB8 / (1S,3R,8AS)-8-(2-{(4S,6S)-3-(4-HYDROXY-3-METHOXYBENZYL)-4-[2-(METHYLAMINO)-2-OXOETHYL]-2-OXO-1,3-OXAZINAN-6-YL}ETHYL)-3 ,7-DIMETHYL-1,2,3,7,8,8A-HEXAHYDRONAPHTHALEN-1-YL (2R)-2-METHYLBUTANOATE / LFA878 / (S)-2-METHYL-BUTYRIC ACID (1S,3R,7S,8S,8AR)-8-{2-[(4R,6R)-3-(4-HYDROXY-3-METHOXY-BENZYL)-4-METHYLCARBAMOYLMETHYL-2-OXO-[1,3]OXAZINAN-6-YL]-ETHYL}- 3,7-DIMETHYL-1,2,3,7,8,8A-HEXAHYDRO-NAPHTHALEN-1-YL ESTER


Mass: 596.754 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H48N2O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.2 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium citrate, ammonium acetate, glycerol, PEG4000, pH 5.6, 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: 2.1→8 Å / Num. all: 29635 / Num. obs: 29635 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.067 / Net I/σ(I): 22.5
Reflection shellResolution: 2.1→2.17 Å / Mean I/σ(I) obs: 6.5 / Rsym value: 0.236 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CQP

1cqp


Resolution: 2.1→8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.804 / SU ML: 0.382 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21276 1492 5 %RANDOM
Rwork0.19096 ---
obs0.19205 28105 98.3 %-
all-28105 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.077 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2---1.72 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2936 0 88 148 3172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223090
X-RAY DIFFRACTIONr_bond_other_d0.0010.022730
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9884168
X-RAY DIFFRACTIONr_angle_other_deg0.78336390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5663362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03215572
X-RAY DIFFRACTIONr_chiral_restr0.0820.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023326
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02602
X-RAY DIFFRACTIONr_nbd_refined0.2070.3573
X-RAY DIFFRACTIONr_nbd_other0.2040.32519
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.5155
X-RAY DIFFRACTIONr_metal_ion_refined0.0730.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.319
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.59
X-RAY DIFFRACTIONr_mcbond_it1.0771.51812
X-RAY DIFFRACTIONr_mcangle_it1.92222936
X-RAY DIFFRACTIONr_scbond_it2.59131278
X-RAY DIFFRACTIONr_scangle_it4.3624.51232
LS refinement shellResolution: 2.1→2.151 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.277 85
Rwork0.233 1862

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