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- PDB-1yfm: RECOMBINANT YEAST FUMARASE -

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Basic information

Entry
Database: PDB / ID: 1yfm
TitleRECOMBINANT YEAST FUMARASE
ComponentsFUMARASE
KeywordsLYASE / FUMARASE / KREBS CYCLE / ACTIVE SITE WATER / HYDRATASE / MULTI-SUBUNIT ACTIVE SITE
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / tricarboxylic acid cycle / double-strand break repair / mitochondrial matrix / DNA damage response ...Citric acid cycle (TCA cycle) / tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / tricarboxylic acid cycle / double-strand break repair / mitochondrial matrix / DNA damage response / mitochondrion / nucleus / cytosol
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 ...Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / 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 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fumarate hydratase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWeaver, T.M. / Lees, M.R. / Banaszak, L.J.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Crystal structures of native and recombinant yeast fumarase.
Authors: Weaver, T. / Lees, M. / Zaitsev, V. / Zaitseva, I. / Duke, E. / Lindley, P. / McSweeny, S. / Svensson, A. / Keruchenko, J. / Keruchenko, I. / Gladilin, K. / Banaszak, L.
History
DepositionJan 7, 1998Processing site: BNL
Revision 1.0Jul 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FUMARASE


Theoretical massNumber of molelcules
Total (without water)53,2451
Polymers53,2451
Non-polymers00
Water0
1
A: FUMARASE

A: FUMARASE

A: FUMARASE

A: FUMARASE


Theoretical massNumber of molelcules
Total (without water)212,9794
Polymers212,9794
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation7_558y,x,-z+31
crystal symmetry operation8_778-y+2,-x+2,-z+31
Buried area27450 Å2
ΔGint-149 kcal/mol
Surface area57590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.190, 95.190, 100.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein FUMARASE / / YFUM


Mass: 53244.672 Da / Num. of mol.: 1 / Mutation: K289R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FUM1 / Plasmid: PASKYMFUM / Cellular location (production host): CYTOPLASM / Gene (production host): FUM1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P08417, fumarate hydratase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 50 %
Crystal growpH: 8.3
Details: 150 MM TRIS-HCL PH 8.3, 100 MM LI2SO4, 8-10% PEG 4000
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1150 mMTris-HCl11
2100 mM11Li2SO4
38-10 %PEG400011

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.59→10 Å / Num. obs: 14127 / % possible obs: 94.5 % / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Rmerge(I) obs: 0.109 / Rsym value: 0.154 / Net I/σ(I): 6.9
Reflection shellResolution: 2.59→2.62 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 0.487 / Rsym value: 0.54 / % possible all: 67
Reflection
*PLUS
Num. measured all: 118256
Reflection shell
*PLUS
% possible obs: 66.7 %

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FUO

1fuo


Resolution: 2.6→30 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.315 2558 10 %RANDOM
Rwork0.196 ---
obs0.196 14127 60 %-
Displacement parametersBiso mean: 24.3 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 0 0 3439
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.94
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.5
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
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8 /
Num. reflection% reflection
Rwork57 -
obs-60 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 11555
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.94
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.5

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