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- PDB-1hb6: Structure of bovine Acyl-CoA binding protein in orthorhombic crys... -

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Basic information

Entry
Database: PDB / ID: 1hb6
TitleStructure of bovine Acyl-CoA binding protein in orthorhombic 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 / Golgi apparatus / endoplasmic reticulum
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 (cattle)
MethodX-RAY DIFFRACTION / 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 1.3Dec 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0442
Polymers9,9311
Non-polymers1121
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)26.050, 54.780, 65.830
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 ACYL-COA BINDING PROTEIN / ACBP / DIAZEPAM BINDING INHIBITOR / DBI ENDOZEPINE / EP


Mass: 9931.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) BOS TAURUS (cattle) / References: UniProt: P07107
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 47.99 %
Crystal growpH: 7.5 / Details: 15% PEG8000, 5MMCDCL2, 10MM HEPES PH7.5, pH 7.50

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: MULTIWIRE UCSD / Detector: AREA DETECTOR / Date: Aug 15, 1991
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→19 Å / Num. obs: 6473 / % possible obs: 94.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 32
Reflection shellResolution: 2→2.15 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 9.3 / % possible all: 91.2

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Processing

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

2abd


Resolution: 2→19.14 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 279496.71 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.226 647 10.1 %RANDOM
Rwork0.2 ---
obs0.2 6394 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.5548 Å2 / ksol: 0.309179 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å20 Å20 Å2
2---2.9 Å20 Å2
3---0.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-20 Å
Luzzati sigma a0.18 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2→19.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms698 0 1 60 759
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it3.142
X-RAY DIFFRACTIONc_scangle_it4.632.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.271 79 10.9 %
Rwork0.206 645 -
obs--89.1 %
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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