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- PDB-1nis: CRYSTAL STRUCTURE OF ACONITASE WITH TRANS-ACONITATE AND NITROCITR... -

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Basic information

Entry
Database: PDB / ID: 1nis
TitleCRYSTAL STRUCTURE OF ACONITASE WITH TRANS-ACONITATE AND NITROCITRATE BOUND
ComponentsACONITASE
KeywordsLYASE(CARBON-OXYGEN)
Function / homology
Function and homology information


Maturation of TCA enzymes and regulation of TCA cycle / Citric acid cycle (TCA cycle) / aconitate hydratase / aconitate hydratase activity / citrate metabolic process / 3 iron, 4 sulfur cluster binding / Mitochondrial protein degradation / tricarboxylic acid cycle / ferrous iron binding / 4 iron, 4 sulfur cluster binding ...Maturation of TCA enzymes and regulation of TCA cycle / Citric acid cycle (TCA cycle) / aconitate hydratase / aconitate hydratase activity / citrate metabolic process / 3 iron, 4 sulfur cluster binding / Mitochondrial protein degradation / 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, 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
2-HYDROXY-2-NITROMETHYL SUCCINIC ACID / 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. / Beinert, H. / Stout, C.D.
Citation
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.
#1: Journal: Biochemistry / Year: 1992
Title: Crystal Structure of Aconitase with Isocitrate and Nitroisocitrate Bound
Authors: Lauble, H. / Kennedy, M.C. / Beinert, H. / Stout, C.D.
#2: 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.
#3: Journal: Proteins / Year: 1989
Title: The Structure of Aconitase
Authors: Robbins, A.H. / Stout, C.D.
#4: 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.
History
DepositionJan 17, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details

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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)83,3633
Polymers82,8181
Non-polymers5452
Water5,224290
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MB112
Atom site foot note1: RESIDUE 325 IS A CIS PROLINE. / 2: SEE REMARK 5.

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Components

#1: Protein ACONITASE


Mass: 82818.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P20004, aconitate hydratase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-NTC / 2-HYDROXY-2-NITROMETHYL SUCCINIC ACID


Mass: 193.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7NO7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion / Details: seeding
Components of the solutions
*PLUS
IDConc.Common 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

Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 20 Å / Num. all: 59472 / Num. obs: 50474 / % possible obs: 85.6 % / Num. measured all: 286813 / Rmerge(I) obs: 0.067

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.05→8 Å / σ(F): 0
Details: RESIDUE 647 IS ARG FROM THE DNA SEQUENCE, (H. ZALKIN, PRIVATE COMMUNICATION) BUT CANNOT BE ACCOMMODATED AS SUCH IN THE STRUCTURE. IT HAS BEEN MODELED AS SER, BASED ON THE EXTENT OF THE SIDE ...Details: RESIDUE 647 IS ARG FROM THE DNA SEQUENCE, (H. ZALKIN, PRIVATE COMMUNICATION) BUT CANNOT BE ACCOMMODATED AS SUCH IN THE STRUCTURE. IT HAS BEEN MODELED AS SER, BASED ON THE EXTENT OF THE SIDE CHAIN DENSITY. ATOMS ARE IN ORTHOGONAL ANGSTROMS COORDINATES IN B2 WITH X ALONG A, Y ALONG B, Z ALONG C.
RfactorNum. reflection
Rwork0.172 -
obs0.172 48708
Refinement stepCycle: LAST / Resolution: 2.05→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5812 0 26 292 6130
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_deg3.06
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
Refinement
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 8 Å / Num. reflection all: 48708 / σ(I): 0 / Rfactor all: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d

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