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- PDB-1fup: FUMARASE WITH BOUND PYROMELLITIC ACID -

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Basic information

Entry
Database: PDB / ID: 1fup
TitleFUMARASE WITH BOUND PYROMELLITIC ACID
ComponentsFUMARASE C
KeywordsLYASE / TRICARBOXYLIC ACID CYCLE
Function / homology
Function and homology information


fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / tricarboxylic acid cycle / response to oxidative stress / identical protein binding / cytoplasm
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarate lyase, conserved site ...Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
D-MALATE / PYROMELLITIC ACID / Fumarate hydratase class II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsWeaver, T. / Banaszak, L.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystallographic studies of the catalytic and a second site in fumarase C from Escherichia coli.
Authors: Weaver, T. / Banaszak, L.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: The Multisubunit Active Site of Fumarase C from Escherichia Coli
Authors: Weaver, T.M. / Levitt, D.G. / Donnelly, M.I. / Stevens, P.P. / Banaszak, L.J.
History
DepositionAug 29, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: FUMARASE C
B: FUMARASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2556
Polymers102,4792
Non-polymers7764
Water6,251347
1
A: FUMARASE C
B: FUMARASE C
hetero molecules

A: FUMARASE C
B: FUMARASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,51112
Polymers204,9584
Non-polymers1,5538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Buried area30880 Å2
ΔGint-189 kcal/mol
Surface area54190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.000, 219.900, 86.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTWO SUBUNITS OF FUMARASE C ARE PRESENT IN THE ASU. THE MOLECULE IS A TETRAMER AND TRANSFORMATION MATRIX/VECTOR FOR GENERATING THE OTHER 2 SUBUNITS IS GIVEN. IN ONE SUBUNIT RESIDUES 317 - 320 ARE MISSING DUE TO A BREAK IN THE ELECTRON DENSITY. ALTHOUGH THIS IS A RECOMBINANT PROTEIN WITH A FIVE HISTIDINE ARM ON THE C-TERMINAL, NO ELECTRON DENSITY WAS SEEN TO ACCOUNT FOR THESE RESIDUES. THE CRYSTALLINE PROTEIN INCLUDES COORDINATES FOR A MALATE AND PYROMELLITIC ACID OBSERVED IN THE ELECTRON DENSITY AND DESCRIBED FULLY IN THE BIOCHEMISTRY REFERENCE.

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Components

#1: Protein FUMARASE C / FUMC


Mass: 51239.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PEFC001 / Gene (production host): FUMARASE C / Production host: Escherichia coli (E. coli) / References: UniProt: P05042, fumarate hydratase
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-PMA / PYROMELLITIC ACID


Mass: 254.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H6O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUES IN AND AROUND THR 96, HIS 129, SER 139, HIS 188, THR 230, LYS 324, AND LEU 358 ARE ALL ...RESIDUES IN AND AROUND THR 96, HIS 129, SER 139, HIS 188, THR 230, LYS 324, AND LEU 358 ARE ALL INVOLVED IN CONTACTS DIRECTLY OR INDIRECTLY WITH EITHER LIGAND AT EITHER THE ACTIVE SITE OR B-SITE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 50 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1300 mMcitrate1reservoir
214 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 44413 / % possible obs: 98.5 % / Redundancy: 6.34 % / Rmerge(I) obs: 0.0732

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 2.3→8 Å
RfactorNum. reflection
Rfree0.234 -
Rwork0.185 -
obs0.185 64254
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6904 0 54 347 7305
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.253
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.02
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.257
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.02
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.257

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