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- PDB-1amj: STERIC AND CONFORMATIONAL FEATURES OF THE ACONITASE MECHANISM -

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Basic information

Entry
Database: PDB / ID: 1amj
TitleSTERIC AND CONFORMATIONAL FEATURES OF THE ACONITASE MECHANISM
ComponentsACONITASE
KeywordsLYASE(CARBON-OXYGEN)
Function / homologyAconitase, mitochondrial-like / Aconitase/3-isopropylmalate dehydratase, swivel / Citric acid cycle (TCA cycle) / Aconitase family signature 2. / Aconitase family signature 1. / Aconitase C-terminal domain / Aconitase family (aconitate hydratase) / Aconitase, iron-sulfur domain / Aconitase family, 4Fe-4S cluster binding site / Aconitase, domain 2 ...Aconitase, mitochondrial-like / Aconitase/3-isopropylmalate dehydratase, swivel / Citric acid cycle (TCA cycle) / Aconitase family signature 2. / Aconitase family signature 1. / Aconitase C-terminal domain / Aconitase family (aconitate hydratase) / Aconitase, iron-sulfur domain / Aconitase family, 4Fe-4S cluster binding site / Aconitase, domain 2 / Aconitase A/isopropylmalate dehydratase small subunit, swivel domain / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 / aconitate hydratase / aconitate hydratase activity / citrate metabolic process / 3 iron, 4 sulfur cluster binding / ferrous iron binding / tricarboxylic acid cycle / 4 iron, 4 sulfur cluster binding / myelin sheath / iron ion binding / mitochondrion / Aconitate hydratase, mitochondrial
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / 2 Å resolution
AuthorsStout, C.D.
Citation
Journal: Proteins / Year: 1995
Title: Steric and conformational features of the aconitase mechanism.
Authors: Lauble, H. / Stout, C.D.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal Structures of Aconitase with Trans-Aconitate and Nitrocitrate Bound
Authors: Lauble, H. / Kennedy, M.C. / Beinert, H. / Stout, C.D.
#2: Journal: Biochemistry / Year: 1992
Title: Crystal Structures of Aconitase with Isocitrate and Nitroisocitrate Bound
Authors: Lauble, H. / Kennedy, M.C. / Beinert, H. / Stout, C.D.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: Structure of Activated Aconitase. Formation of the (4Fe-4S) Cluster in the Crystal
Authors: Robbins, A.H. / Stout, C.D.
#4: Journal: Proteins / Year: 1989
Title: The Structure of Aconitase
Authors: Robbins, A.H. / Stout, C.D.
#5: Journal: J.Biol.Chem. / Year: 1985
Title: Iron-Sulfur Cluster in Aconitase. Crystallographic Evidence for a Three-Iron Center
Authors: Robbins, A.H. / Stout, C.D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 11, 1994 / Release: Jan 26, 1995
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 26, 1995Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Nov 29, 2017Structure modelDerived calculations / Otherpdbx_database_status / struct_conf / struct_conf_type_pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACONITASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2304
Polyers82,7651
Non-polymers4653
Water6,395355
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)185.500, 72.000, 73.000
Angle α, β, γ (deg.)90.00, 90.00, 77.70
Int Tables number5
Space group name H-MB 1 1 2
Atom site foot note1: CIS PROLINE - PRO 325

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Components

#1: Protein/peptide ACONITASE /


Mass: 82764.938 Da / Num. of mol.: 1 / Source: (gene. exp.) Bos taurus (cattle) / Genus: Bos / References: UniProt: P20004, aconitate hydratase
#2: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Formula: HO / Hydroxide
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Formula: SO4 / Sulfate
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Formula: Fe4S4 / Iron–sulfur cluster
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 / Density percent sol: 57.23 %
Crystal grow
*PLUS
Temp: 22 ℃ / pH: 7 / Method: vapor diffusion
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
13.7 Mammonium sulfate1drop
20.5 MTris-HCl1drop
32.2 Mammonium sulfate1reservoir
40.5 MTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNumber obs: 213254 / Observed criterion sigma I: 0 / Percent possible obs: 92.4
Reflection
*PLUS
D resolution high: 2 Å / Number obs: 58806 / Number measured all: 213254 / Rmerge I obs: 0.076
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / Percent possible obs: 43.4 / MeanI over sigI obs: 2.8

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefineSigma F: 0
Displacement parametersB iso mean: 21.1 Å2
Least-squares processR factor R work: 0.168 / R factor obs: 0.168 / Highest resolution: 2 Å / Lowest resolution: 8 Å / Number reflection obs: 57828
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 5812 / Nucleic acid: 0 / Ligand: 15 / Solvent: 355 / Total: 6182
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_d1.42
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 / Classification: refinement
Least-squares process
*PLUS
R factor all: 0.168 / Number reflection all: 57828
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.01

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