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- PDB-1fgh: COMPLEX WITH 4-HYDROXY-TRANS-ACONITATE -

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Basic information

Entry
Database: PDB / ID: 1fgh
TitleCOMPLEX WITH 4-HYDROXY-TRANS-ACONITATE
ComponentsACONITASE
KeywordsLYASE / COMPLEX
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / aconitate hydratase / aconitate hydratase activity / citrate metabolic process / 3 iron, 4 sulfur cluster binding / tricarboxylic acid cycle / ferrous iron binding / 4 iron, 4 sulfur cluster binding / iron ion binding / mitochondrion / 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
4-HYDROXY-ACONITATE ION / IRON/SULFUR CLUSTER / Aconitate hydratase, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsLauble, H. / Kennedy, M.C. / Emptage, M.H. / Beinert, H. / Stout, C.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: The reaction of fluorocitrate with aconitase and the crystal structure of the enzyme-inhibitor complex.
Authors: Lauble, H. / Kennedy, M.C. / Emptage, M.H. / Beinert, H. / Stout, C.D.
History
DepositionSep 14, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _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.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_ref_seq_dif.details / _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: ACONITASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2873
Polymers82,7481
Non-polymers5392
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.900, 71.800, 72.200
Angle α, β, γ (deg.)90.00, 90.00, 77.70
Int Tables number5
Space group name H-MB112

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Components

#1: Protein ACONITASE /


Mass: 82747.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: [4FE-4S] BOUND BY CYS 358, CYS 421, CYS 424 / Source: (natural) Bos taurus (cattle) / Organ: HEART / Tissue: HEART MITOCHONDRIA / References: UniProt: P20004, aconitate hydratase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-ATH / 4-HYDROXY-ACONITATE ION


Mass: 187.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H3O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 57 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
116.4 mg/mlenzyme1drop
21.5 mMfluorocitrate1drop
325 mMHEPES1drop
515 mMtricarballylate1drop
60.35 M1dropNaCl
70.25 Mbis-Tris-HCl1drop
82.2 M1reservoir(NH4)SO4
95 mMtricarballylate1reservoir
100.35 M1reservoirNaCl
110.25 Mbis-Tris-HCl1reservoir
41drop(NH4)SO40.018ml saturated

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 52746 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.06
Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 20 Å / Num. measured all: 267668 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 2.23 Å / % possible obs: 47 % / Rmerge(I) obs: 0.032

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.05→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.177 -
obs0.177 52746
Refinement stepCycle: LAST / Resolution: 2.05→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5812 0 26 256 6094
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg3.01
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

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