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- PDB-1hb8: Structure of bovine Acyl-CoA binding protein in tetragonal crysta... -

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Basic information

Entry
Database: PDB / ID: 1hb8
TitleStructure of bovine Acyl-CoA binding protein in tetragonal crystal form
ComponentsACYL-COA BINDING PROTEIN
KeywordsACYL-COENZYME A BINDING PROTEIN / ACYL-COA / BINDING PROTEIN
Function / homology
Function and homology information


Mitochondrial Fatty Acid Beta-Oxidation / fatty-acyl-CoA binding / fatty acid metabolic process / endoplasmic reticulum / Golgi apparatus
Similarity search - Function
Acyl-CoA-binding protein, ACBP, conserved site / Acyl-CoA-binding (ACB) domain signature. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / FERM/acyl-CoA-binding protein superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Acyl-CoA-binding protein
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZou, J.Y. / Kleywegt, G.J. / Bergfors, T. / Knudsen, J. / Jones, T.A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Binding Site Differences Revealed by Crystal Structures of Plasmodium Falciparum and Bovine Acyl-Coa Binding Protein
Authors: Van Aalten, D.M.F. / Milne, K.G. / Zou, J.Y. / Kleywegt, G.J. / Bergfors, T. / Ferguson, M.A.J. / Knudsen, J. / Jones, T.A.
History
DepositionApr 12, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2002Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ACYL-COA BINDING PROTEIN
B: ACYL-COA BINDING PROTEIN
C: ACYL-COA BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0826
Polymers29,7943
Non-polymers2883
Water3,801211
1
A: ACYL-COA BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0272
Polymers9,9311
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ACYL-COA BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0272
Polymers9,9311
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ACYL-COA BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0272
Polymers9,9311
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.780, 47.780, 128.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999822, 0.009537, -0.016268), (-0.009254, -0.503519, -0.863935), (-0.01643, 0.863932, -0.503341)17.542, -60.153, 149.632
2given(0.999924, 0.000533, -0.012298), (0.010967, -0.492228, 0.870397), (-0.00559, -0.870466, -0.492196)-15.532, 99.253, 126.374

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Components

#1: Protein ACYL-COA BINDING PROTEIN / ACBP / DIAZEPAM BINDING INHIBITOR / DBI ENDOZEPINE / EP


Mass: 9931.289 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) BOS TAURUS (domestic cattle) / References: UniProt: P07107
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMAY FUNCTION AS AN INTRACELLULAR CARRIER OF ACYL-COA ESTERS. IT ALSO DISPLACES DIAZEPAM FROM THE ...MAY FUNCTION AS AN INTRACELLULAR CARRIER OF ACYL-COA ESTERS. IT ALSO DISPLACES DIAZEPAM FROM THE BENZODIAZEPINE (BZD) RECOGNITION SITE LOCATED ON THE GABA TYPE A RECEPTOR. IT IS THEREFORE POSSIBLE THAT IT MODULATES THE ACTION OF THE GABA RECEPTOR.

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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: 2.4 Å3/Da / Density % sol: 50.15 %
Crystal growpH: 7.5
Details: 25% PEG5000 MME, 40MM NI(SO4)2, 40MM HEPES PH7.5, pH 7.50

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.928
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 18831 / % possible obs: 96.5 % / Redundancy: 2.7 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.6 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ABD

2abd


Resolution: 2→19.13 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1235568.81 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 941 5 %RANDOM
Rwork0.223 ---
obs0.223 18784 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4456 Å2 / ksol: 0.384682 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2--1.22 Å20 Å2
3----2.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-20 Å
Luzzati sigma a0.26 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→19.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 15 211 2320
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.172
X-RAY DIFFRACTIONc_mcangle_it1.652.5
X-RAY DIFFRACTIONc_scbond_it2.163
X-RAY DIFFRACTIONc_scangle_it3.143.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.328 128 5.4 %
Rwork0.297 2261 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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