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- PDB-1bhq: MAC-1 I DOMAIN CADMIUM COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1bhq
TitleMAC-1 I DOMAIN CADMIUM COMPLEX
ComponentsCD11B
KeywordsCELL ADHESION / INTEGRIN / I DOMAIN
Function / homology
Function and homology information


ectodermal cell differentiation / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / response to curcumin / integrin alphaM-beta2 complex / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning / complement-mediated synapse pruning ...ectodermal cell differentiation / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / response to curcumin / integrin alphaM-beta2 complex / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning / complement-mediated synapse pruning / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / complement receptor mediated signaling pathway / heterotypic cell-cell adhesion / integrin complex / cargo receptor activity / cell adhesion mediated by integrin / phagocytosis, engulfment / plasma membrane raft / amyloid-beta clearance / tertiary granule membrane / positive regulation of protein targeting to membrane / Integrin cell surface interactions / response to mechanical stimulus / specific granule membrane / forebrain development / heat shock protein binding / cell-matrix adhesion / receptor-mediated endocytosis / positive regulation of superoxide anion generation / integrin-mediated signaling pathway / response to ischemia / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / integrin binding / response to estradiol / amyloid-beta binding / Interleukin-4 and Interleukin-13 signaling / cell adhesion / external side of plasma membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / 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-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / 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
ACETYL GROUP / : / Integrin alpha-M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / ISOMORPHOUS TO KNOWN PDB ENTRY 1IDN / Resolution: 2.7 Å
AuthorsBaldwin, E.T.
CitationJournal: Structure / Year: 1998
Title: Cation binding to the integrin CD11b I domain and activation model assessment
Authors: Baldwin, E.T. / Sarver, R.W. / Bryant Jr., G.L. / Curry, K.A. / Fairbanks, M.B. / Finzel, B.C. / Garlick, R.L. / Heinrikson, R.L. / Horton, N.C. / Kelley, L.L. / Mildner, A.M. / Moon, J.B. / ...Authors: Baldwin, E.T. / Sarver, R.W. / Bryant Jr., G.L. / Curry, K.A. / Fairbanks, M.B. / Finzel, B.C. / Garlick, R.L. / Heinrikson, R.L. / Horton, N.C. / Kelley, L.L. / Mildner, A.M. / Moon, J.B. / Mott, J.E. / Mutchler, V.T. / Tomich, C.S. / Watenpaugh, K.D. / Wiley, V.H.
History
DepositionJun 10, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _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
1: CD11B
2: CD11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7537
Polymers43,3282
Non-polymers4255
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.420, 122.390, 75.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9621, 0.2721, 0.0068), (0.2727, 0.9621, 0.0016), (-0.0065, 0.0021, -0.9999)
Vector: -0.0341, -0.0614, 43.648)

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Components

#1: Protein CD11B / CELL SURFACE GLYCOPROTEIN MAC-1 ALPHA SUBUNIT


Mass: 21663.799 Da / Num. of mol.: 2 / Fragment: MAC-1 ALPHA DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSE / References: UniProt: P11215
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.48 Å3/Da / Density % sol: 49 %
Description: DATA WERE COLLECTED BY OSCILLATION WITH 0.25 DEGREE FRAME WIDTHS
Crystal growMethod: vapor diffusion, sitting drop / pH: 5
Details: CRYSTALS WERE GROWN BY VAPOR DIFFUSION ON SITTING DROP BRIDGES. THE WELL MIX OF 20-24% PEG6000 BUFFERED WITH 100 MM NA ACETATE PH 5.0 WAS MIXED 1:1 WITH 3 UL OF I DOMAIN PROTEIN (20-30 ...Details: CRYSTALS WERE GROWN BY VAPOR DIFFUSION ON SITTING DROP BRIDGES. THE WELL MIX OF 20-24% PEG6000 BUFFERED WITH 100 MM NA ACETATE PH 5.0 WAS MIXED 1:1 WITH 3 UL OF I DOMAIN PROTEIN (20-30 MG/ML, 50 MM HEPES PH 7.0, 0.025% NA AZIDE). CRYSTALS WERE STABLIZED IN 10MM CDCL2, 100 MM NA ACETATE 5.0, 26% PEG6000 FOR DATA COLLECTION., vapor diffusion - sitting drop
PH range: 5.0-7.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: reservoir was mixed 1:1 with 3 microlitter protein
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-30 mg/mlprotein1drop
250 mMHEPES1drop
30.025 %sodium azide1drop
420-24 %PEG60001reservoir
5100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→10 Å / Num. obs: 7424 / % possible obs: 43.9 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rsym value: 0.097 / Net I/σ(I): 10.6
Reflection shellResolution: 2.65→2.91 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.192 / % possible all: 43.3
Reflection
*PLUS
Num. obs: 8618 / Num. measured all: 26642 / Rmerge(I) obs: 0.097

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Processing

Software
NameClassification
PROLSQrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: ISOMORPHOUS TO KNOWN PDB ENTRY 1IDN
Starting model: CD11B I DOMAIN METAL FREE PDB ENTRY 1IDN

1idn


Resolution: 2.7→10 Å / σ(F): 2
Details: PARAMETERS FROM SIELECKI ET AL. JMB 134, 781-804 1979
RfactorNum. reflection% reflection
Rwork0.175 --
obs0.175 8618 43.9 %
Displacement parametersBiso mean: 10.63 Å2
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3059 0 2 139 3200
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.03
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.5521.5
X-RAY DIFFRACTIONp_mcangle_it0.9643
X-RAY DIFFRACTIONp_scbond_it0.7962
X-RAY DIFFRACTIONp_scangle_it1.3414
X-RAY DIFFRACTIONp_plane_restr0.0130.03
X-RAY DIFFRACTIONp_chiral_restr0.2010.2
X-RAY DIFFRACTIONp_singtor_nbd0.1970.4
X-RAY DIFFRACTIONp_multtor_nbd0.2590.4
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2560.4
X-RAY DIFFRACTIONp_planar_tor2.23
X-RAY DIFFRACTIONp_staggered_tor9.15
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2110
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 7424
Solvent computation
*PLUS
Displacement parameters
*PLUS

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