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- PDB-2fj9: High resolution crystal structure of the unliganded human ACBP -

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Basic information

Entry
Database: PDB / ID: 2fj9
TitleHigh resolution crystal structure of the unliganded human ACBP
ComponentsAcyl-CoA-binding protein
KeywordsLIPID BINDING PROTEIN / FATTY ACID METABOLISM / ACBP
Function / homology
Function and homology information


negative regulation of protein lipidation / benzodiazepine receptor binding / protein-lipid complex / long-chain fatty acyl-CoA binding / positive regulation of phospholipid transport / phosphatidylcholine acyl-chain remodeling / fatty-acyl-CoA binding / perinuclear endoplasmic reticulum / Mitochondrial Fatty Acid Beta-Oxidation / positive regulation of CoA-transferase activity ...negative regulation of protein lipidation / benzodiazepine receptor binding / protein-lipid complex / long-chain fatty acyl-CoA binding / positive regulation of phospholipid transport / phosphatidylcholine acyl-chain remodeling / fatty-acyl-CoA binding / perinuclear endoplasmic reticulum / Mitochondrial Fatty Acid Beta-Oxidation / positive regulation of CoA-transferase activity / fatty acid metabolic process / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / extracellular exosome / identical protein binding
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
LEAD (II) ION / Acyl-CoA-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsTaskinen, J.P. / van Aalten, D.M. / Knudsen, J. / Wierenga, R.K.
CitationJournal: Proteins / Year: 2006
Title: High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl-CoA ligand.
Authors: Taskinen, J.P. / van Aalten, D.M. / Knudsen, J. / Wierenga, R.K.
History
DepositionJan 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.5Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.ptnr1_symmetry / _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.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

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Assembly

Deposited unit
A: Acyl-CoA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2745
Polymers9,9301
Non-polymers3444
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Acyl-CoA-binding protein
hetero molecules

A: Acyl-CoA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,54810
Polymers19,8602
Non-polymers6878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area1150 Å2
ΔGint-78 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.824, 43.824, 177.247
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-88-

ZN

21A-1277-

HOH

31A-1325-

HOH

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Components

#1: Protein Acyl-CoA-binding protein / / ACBP / Diazepam-binding inhibitor / DBI / Endozepine / EP


Mass: 9930.243 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DBI / Production host: Escherichia coli (E. coli) / References: UniProt: P07108
#2: Chemical ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG-MME 550, 100mM MES, pH 6.5, 10mM ZnSO4, 3% 1-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 2, 2000
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.56→30 Å / Num. all: 13635 / Num. obs: 14797 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.052 / Net I/σ(I): 31.9
Reflection shellResolution: 1.56→1.62 Å / Rsym value: 0.211 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→14.83 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1278929.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 479 3.5 %RANDOM
Rwork0.196 ---
obs0.196 13635 95.9 %-
all-14797 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.9946 Å2 / ksol: 0.333733 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å2-0.18 Å20 Å2
2--4.61 Å20 Å2
3----5.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→14.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms698 0 4 228 930
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d2.67
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 87 3.8 %
Rwork0.242 2183 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4ion.param

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