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- PDB-6ejx: The metal ion-dependent adhesion site (MIDAS) of the alphaMbeta2 ... -

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Basic information

Entry
Database: PDB / ID: 6ejx
TitleThe metal ion-dependent adhesion site (MIDAS) of the alphaMbeta2 integrin Mac-1 I-domain promiscuously and competitively binds multiple ligands in the regulation of Leukocyte function
ComponentsPlatelet glycoprotein Ib alpha chain
KeywordsBLOOD CLOTTING / Gp1balpha / Mac-1
Function / homology
Function and homology information


GP1b-IX-V activation signalling / : / Platelet Adhesion to exposed collagen / Platelet Aggregation (Plug Formation) / Intrinsic Pathway of Fibrin Clot Formation / hemostasis / plasma membrane => GO:0005886 / fibrinolysis / extracellular matrix / cell morphogenesis ...GP1b-IX-V activation signalling / : / Platelet Adhesion to exposed collagen / Platelet Aggregation (Plug Formation) / Intrinsic Pathway of Fibrin Clot Formation / hemostasis / plasma membrane => GO:0005886 / fibrinolysis / extracellular matrix / cell morphogenesis / platelet aggregation / blood coagulation / cell adhesion / extracellular space / membrane / plasma membrane
Similarity search - Function
Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat ...Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / DI(HYDROXYETHYL)ETHER / N-PROPANOL / Platelet glycoprotein Ib alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEmsley, J. / Saleem, M.
CitationJournal: Blood Adv / Year: 2019
Title: Structural basis of the leukocyte integrin Mac-1 I-domain interactions with the platelet glycoprotein Ib.
Authors: Morgan, J. / Saleem, M. / Ng, R. / Armstrong, C. / Wong, S.S. / Caulton, S.G. / Fickling, A. / Williams, H.E.L. / Munday, A.D. / Lopez, J.A. / Searle, M.S. / Emsley, J.
History
DepositionSep 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Platelet glycoprotein Ib alpha chain
A: Platelet glycoprotein Ib alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,55115
Polymers62,2792
Non-polymers1,27213
Water9,296516
1
D: Platelet glycoprotein Ib alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5104
Polymers31,1401
Non-polymers3703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Platelet glycoprotein Ib alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,04111
Polymers31,1401
Non-polymers90110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.537, 72.870, 164.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules DA

#1: Protein Platelet glycoprotein Ib alpha chain / Glycoprotein Ibalpha


Mass: 31139.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gp1ba
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: O35930

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Non-polymers , 6 types, 529 molecules

#2: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-POL / N-PROPANOL / 1-PROPONOL / Propan-1-ol


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% v/v Ethylene glycol; 10 % w/v PEG 8000 0.1M Imidazole; MES monohydrate (acid) 0.02M 1,6-Hexanediol; 0.02M 1-Butanol; 0.02M 1,2-Propanediol; 0.02M 2- Propanol; 0.02M 1,4-Butanediol; 0.02M 1,3-Propanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2→49.22 Å / Num. obs: 48095 / % possible obs: 98.67 % / Redundancy: 3.66 % / Net I/σ(I): 5.3
Reflection shellHighest resolution: 2 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P72

3p72


Resolution: 2→49.22 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.459 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23175 1417 2.9 %RANDOM
Rwork0.18402 ---
obs0.18541 48095 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.688 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4175 0 83 516 4774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194382
X-RAY DIFFRACTIONr_bond_other_d0.0030.024103
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.9995966
X-RAY DIFFRACTIONr_angle_other_deg1.08539573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.76525.359181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35815729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2111513
X-RAY DIFFRACTIONr_chiral_restr0.110.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214745
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02808
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5782.8022139
X-RAY DIFFRACTIONr_mcbond_other2.5642.82138
X-RAY DIFFRACTIONr_mcangle_it3.5894.192674
X-RAY DIFFRACTIONr_mcangle_other3.5914.1912675
X-RAY DIFFRACTIONr_scbond_it3.8913.2592243
X-RAY DIFFRACTIONr_scbond_other3.8893.2592243
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9754.7123289
X-RAY DIFFRACTIONr_long_range_B_refined8.08236.085065
X-RAY DIFFRACTIONr_long_range_B_other8.08836.0615063
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 104 -
Rwork0.265 3532 -
obs--98.67 %

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