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- PDB-1b0m: ACONITASE R644Q:FLUOROCITRATE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1b0m
TitleACONITASE R644Q:FLUOROCITRATE COMPLEX
ComponentsPROTEIN (ACONITASE)
KeywordsHYDROLASE / ACONITASE R644Q / FLUOROCITRATE COMPLEX
Function / homology
Function and homology information


aconitate hydratase / aconitate hydratase activity / tricarboxylic acid cycle / 4 iron, 4 sulfur cluster binding / mitochondrion / metal ion binding / cytosol
Similarity search - Function
Aconitase, mitochondrial-like / Aconitase, domain 2 / Aconitase; Domain 2 / Aconitase, Domain 2 / Aconitase; domain 3 / Aconitase, domain 3 / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 / Aconitase family, 4Fe-4S cluster binding site / Aconitase, iron-sulfur domain ...Aconitase, mitochondrial-like / Aconitase, domain 2 / Aconitase; Domain 2 / Aconitase, Domain 2 / Aconitase; domain 3 / Aconitase, domain 3 / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 / Aconitase family, 4Fe-4S cluster binding site / Aconitase, iron-sulfur domain / Aconitase family (aconitate hydratase) / Aconitase family signature 1. / Aconitase family signature 2. / Aconitase; domain 4 / Aconitase, domain 4 / Aconitase A/isopropylmalate dehydratase small subunit, swivel domain / Aconitase C-terminal domain / Aconitase/3-isopropylmalate dehydratase, swivel / Alpha-Beta Barrel / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / IRON/SULFUR CLUSTER / Aconitate hydratase, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLloyd, S.J. / Lauble, H. / Prasad, G.S. / Stout, C.D.
CitationJournal: Protein Sci. / Year: 1999
Title: The mechanism of aconitase: 1.8 A resolution crystal structure of the S642a:citrate complex.
Authors: Lloyd, S.J. / Lauble, H. / Prasad, G.S. / Stout, C.D.
History
DepositionNov 11, 1998Deposition site: BNL / Processing site: RCSB
SupersessionNov 18, 1998ID: 1atq
Revision 1.0Nov 18, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jun 27, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ACONITASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1903
Polymers82,6491
Non-polymers5412
Water6,143341
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.900, 71.900, 73.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (ACONITASE)


Mass: 82648.875 Da / Num. of mol.: 1 / Mutation: R644Q
Source method: isolated from a genetically manipulated source
Details: [4FE-4S] BOUND BY CYS 358, CYS 421, CYS 424 / Source: (gene. exp.) Sus scrofa (pig) / Strain: BL21 DE3 / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / Plasmid: PUC118 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P16276, aconitate hydratase
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details4 STEREOISOMERS OF FLUOROCITRATE, F ATOM NOT SEEN IN DENSITY, H ATOMS NOT MODELED, CARBOXYL GROUPS ...4 STEREOISOMERS OF FLUOROCITRATE, F ATOM NOT SEEN IN DENSITY, H ATOMS NOT MODELED, CARBOXYL GROUPS IONIZED HYDROXYL GROUP BOUND TO FE4 OF [4FE-4S] CLUSTER. OXYGEN ATOM ( O5 ) INCLUDED IN FS4 755
Sequence details1ATQ SWS P16276 1 - 28 NOT IN ATOMS LIST THIS IS RECOMBINANT PORCINE MITOCHONDRIAL ACONITASE - ...1ATQ SWS P16276 1 - 28 NOT IN ATOMS LIST THIS IS RECOMBINANT PORCINE MITOCHONDRIAL ACONITASE - SEQUENCE FOR CDNA KNOWN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 57 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 26 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116-18 mg/mlprotein1drop
20.25 MBis-Tris-HCl1drop
30.35 M1dropNaCl
42.2-2.4 Mammonium sulfate1reservoir
50.25 Mbis-Tris-HCl1reservoir
60.35 M1reservoirNaCl
7ammonium sulfate1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 27625 / % possible obs: 84.9 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rsym value: 0.08 / Net I/σ(I): 5.4
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.277 / % possible all: 83

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
X-PLOR3.8model building
X-PLOR3.8refinement
CCP4data scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FGH

1fgh


Resolution: 2.5→20 Å / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.193 --
obs0.193 27625 84.9 %
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5813 0 22 340 6175
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.65
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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