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- PDB-6acn: STRUCTURE OF ACTIVATED ACONITASE. FORMATION OF THE (4FE-4S) CLUST... -

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Basic information

Entry
Database: PDB / ID: 6acn
TitleSTRUCTURE OF ACTIVATED ACONITASE. FORMATION OF THE (4FE-4S) CLUSTER IN THE CRYSTAL
ComponentsACONITASE
KeywordsLYASE(CARBON-OXYGEN)
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, 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
IRON/SULFUR CLUSTER / TRICARBALLYLIC ACID / Aconitate hydratase, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsRobbins, A.H. / Stout, C.D.
Citation
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.
#1: Journal: Proteins / Year: 1989
Title: The Structure of Aconitase
Authors: Robbins, A.H. / Stout, C.D.
#2: 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 16, 1990Processing site: BNL
Revision 1.0Jul 15, 1990Provider: 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 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn_type.id / _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)83,4134
Polymers82,7891
Non-polymers6243
Water7,332407
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.600, 72.000, 72.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: RESIDUE 325 IS A CIS PROLINE.
2: THE DENSITY FOR THE FOLLOWING REGIONS IS WEAK AND THE FINAL REBUILDING STEPS USED STEREOCHEMICAL CONSIDERATIONS -N-TERMINAL PCA ILE 433 THROUGH GLU 437 THR 488 THROUGH LYS 494 LYS 522 THROUGH GLN ...2: THE DENSITY FOR THE FOLLOWING REGIONS IS WEAK AND THE FINAL REBUILDING STEPS USED STEREOCHEMICAL CONSIDERATIONS -N-TERMINAL PCA ILE 433 THROUGH GLU 437 THR 488 THROUGH LYS 494 LYS 522 THROUGH GLN 527 C-TERMINAL GLN 752 THROUGH LYS 754
3: RESIDUE 647 IS ARG FROM THE DNA SEQUENCE, (H. ZALKIN, PRIVATE COMMUNICATION) BUT CANNOT BE ACCOMODATED AS SUCH IN THE STRUCTURE. IT HAS BEEN MODELLED AS SER, BASED ON THE EXTENT OF THE SIDE CHAIN DENSITY.

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Components

#1: Protein ACONITASE


Mass: 82789.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P16276, aconitate hydratase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-TRC / TRICARBALLYLIC ACID


Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE CONSISTS OF FOUR DOMAINS, THE FIRST THREE ARE TIGHTLY ASSOCIATED AND THE FOURTH ...THE STRUCTURE CONSISTS OF FOUR DOMAINS, THE FIRST THREE ARE TIGHTLY ASSOCIATED AND THE FOURTH ASSOCIATES WITH THE FIRST THREE TO FORM A CLEFT TO THE PUTATIVE ACTIVE SITE. THE FOUR DOMAINS CONSIST OF RESIDUES 1-201, 202-319, 320-512, AND 537-754. RESIDUES 513 TO 536 FORM AN EXTENSIVE LINKER PEPTIDE.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion / Details: referred to J.Biol.Chem. 257.9061-9063 1982
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: 2.5 Å / Lowest resolution: 2.6 Å / Num. obs: 28269 / Num. measured all: 283187 / Rmerge(I) obs: 0.134

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.5→5 Å / Rfactor Rwork: 0.187
Details: RESIDUE 647 IS ARG FROM THE DNA SEQUENCE, (H. ZALKIN, PRIVATE COMMUNICATION) BUT CANNOT BE ACCOMODATED AS SUCH IN THE STRUCTURE. IT HAS BEEN MODELLED 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 ACCOMODATED AS SUCH IN THE STRUCTURE. IT HAS BEEN MODELLED AS SER, BASED ON THE EXTENT OF THE SIDE CHAIN DENSITY. SUBSEQUENT TO PUBLICATION, THE N-TERMINUS HAS BEEN SHOWN TO BE PCA, WHICH REQUIRES THAT ALL SEQUENCE NUMBERS BE REDUCED BY ONE. THUS, THE CYSTEINE LIGANDS TO THE FE4S4 CLUSTER ARE 358, 421, AND 424, RATHER THAN THE PUBLISHED 359,422 AND 425. THE SEQUENCE NUMBERS USED IN THIS ENTRY REFLECT THE N-TERMINAL PCA. THE DENSITY FOR THE FOLLOWING REGIONS IS WEAK AND THE FINAL REBUILDING STEPS USED STEREOCHEMICAL CONSIDERATIONS -N-TERMINAL PCA ILE 433 THROUGH GLU 437 THR 488 THROUGH LYS 494 LYS 522 THROUGH GLN 527 C-TERMINAL GLN 752 THROUGH LYS 754
Refinement stepCycle: LAST / Resolution: 2.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5823 0 25 407 6255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.5
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: 2.5 Å / Lowest resolution: 5 Å / σ(F): 0 / Rfactor all: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.5

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