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- PDB-2fdq: crystal structure of ACBP from Armadillo Harderian Gland -

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Basic information

Entry
Database: PDB / ID: 2fdq
Titlecrystal structure of ACBP from Armadillo Harderian Gland
ComponentsAcyl-CoA-binding protein
KeywordsTRANSPORT PROTEIN / ACBP / Diazepam binding inhibitor
Function / homology
Function and homology information


fatty-acyl-CoA binding / fatty acid metabolic process / Golgi apparatus / endoplasmic reticulum / mitochondrion
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 speciesChaetophractus villosus (large hairy armadillo)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsCostabel, M.D. / Guerin, D.M.A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Structure of armadillo ACBP: a new member of the acyl-CoA-binding protein family.
Authors: Costabel, M.D. / Ermacora, M.R. / Santome, J.A. / Alzari, P.M. / Guerin, D.M.
History
DepositionDec 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-CoA-binding protein
B: Acyl-CoA-binding protein
C: Acyl-CoA-binding protein


Theoretical massNumber of molelcules
Total (without water)29,7253
Polymers29,7253
Non-polymers00
Water66737
1
A: Acyl-CoA-binding protein


Theoretical massNumber of molelcules
Total (without water)9,9081
Polymers9,9081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acyl-CoA-binding protein


Theoretical massNumber of molelcules
Total (without water)9,9081
Polymers9,9081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acyl-CoA-binding protein


Theoretical massNumber of molelcules
Total (without water)9,9081
Polymers9,9081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.110, 49.110, 130.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Acyl-CoA-binding protein / ACBP / EP


Mass: 9908.234 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: Harderian gland
Source: (natural) Chaetophractus villosus (large hairy armadillo)
References: UniProt: P82934
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24% PEG6000, 5% NaCl, 10mM TrisHCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 20, 2001
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→24.56 Å / Num. all: 3911 / Num. obs: 3901 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.5→3.62 Å / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT1.701data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1HB8

1hb8


Resolution: 3.5→24 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 200 5.1 %random
Rwork0.197 ---
all0.244 3901 --
obs0.228 3772 96.6 %-
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 29.26 Å2
Refinement stepCycle: LAST / Resolution: 3.5→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 0 37 2125
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:HOHer_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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