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- PDB-1hbk: Acyl-CoA binding protein from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 1hbk
TitleAcyl-CoA binding protein from Plasmodium falciparum
ComponentsACYL-COA BINDING PROTEIN
KeywordsFATTY ACID METABOLISM
Function / homology
Function and homology information


: / Mitochondrial Fatty Acid Beta-Oxidation / fatty-acyl-CoA binding
Similarity search - Function
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
COENZYME A / MYRISTIC ACID / NICKEL (II) ION / Acyl-CoA binding protein
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
Authorsvan Aalten, D.M.F.
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. / Milne, K.G. / Zou, J.Y. / Kleywegt, G.J. / Bergfors, T. / Ferguson, M.A. / Knudsen, J. / Jones, T.A.
History
DepositionApr 16, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 9, 2019Group: Data collection / Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_sf

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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)11,8035
Polymers10,6901
Non-polymers1,1134
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.665, 48.665, 48.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein ACYL-COA BINDING PROTEIN / ACBP


Mass: 10690.099 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8IK57
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.6 Å3/Da / Density % sol: 54.13 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
250 mMHEPES1drop
3300 mM1dropKCl
410 mM1reservoirNiCl2
5100 mMTris1reservoir
620 %PEG2000 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1
DetectorDate: Nov 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 28928 / % possible obs: 99.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.1
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.9 / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25 Å / Num. obs: 7754 / Num. measured all: 28439 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 95.3 % / Redundancy: 3.4 % / Num. unique obs: 736 / Num. measured obs: 2526 / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.85 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 798970.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 497 6.4 %RANDOM
Rwork0.198 ---
obs0.198 7714 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.6614 Å2 / ksol: 0.356273 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms754 0 45 76 875
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.342.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 76 6 %
Rwork0.261 1194 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3COA.PARCOA.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99

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