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- PDB-1kq7: E315Q Mutant Form of Fumarase C from E.coli -

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Basic information

Entry
Database: PDB / ID: 1kq7
TitleE315Q Mutant Form of Fumarase C from E.coli
ComponentsFUMARATE HYDRATASE CLASS II
KeywordsLYASE / fumarate lyase
Function / homology
Function and homology information


tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / tricarboxylic acid cycle / response to oxidative stress / identical protein binding
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
CITRIC ACID / D-MALATE / Fumarate hydratase class II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWeaver, T.M. / Estevez, M. / Skarda, J. / Spencer, J.
CitationJournal: Protein Sci. / Year: 2002
Title: X-ray crystallographic and kinetic correlation of a clinically observed human fumarase mutation.
Authors: Estevez, M. / Skarda, J. / Spencer, J. / Banaszak, L. / Weaver, T.M.
History
DepositionJan 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FUMARATE HYDRATASE CLASS II
B: FUMARATE HYDRATASE CLASS II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6145
Polymers101,0962
Non-polymers5183
Water32418
1
A: FUMARATE HYDRATASE CLASS II
B: FUMARATE HYDRATASE CLASS II
hetero molecules

A: FUMARATE HYDRATASE CLASS II
B: FUMARATE HYDRATASE CLASS II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,22810
Polymers202,1914
Non-polymers1,0376
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Buried area30530 Å2
ΔGint-186 kcal/mol
Surface area54940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.02, 220.0, 86.23
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
DetailsThe second dimer is generated by application of the following rotation matrix 1.00x 0.00y 0.00z 207.96 0.00x 1.00y 0.00z 0.7685 0.00x 0.00y -1.00z 131.2386

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Components

#1: Protein FUMARATE HYDRATASE CLASS II / E.C.4.2.1.2 / FUMARASE / fumC


Mass: 50547.785 Da / Num. of mol.: 2 / Mutation: Glu 315 to Glutamine
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fumc / Plasmid: pASK40 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P05042, fumarate hydratase
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3350, citrate dithiothreitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 291K
Crystal grow
*PLUS
pH: 5.6 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMTris-HCl11pH7.5
25 mMdithiothreitol11
35 mMEDTA11
4150 mMsodium citrate12pH5.6
514 %PEG335012

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Aug 10, 1998
RadiationMonochromator: graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→11.5 Å / Num. all: 22978 / Num. obs: 24817 / % possible obs: 92.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 16.05 Å2 / Rmerge(I) obs: 0.1121 / Rsym value: 0.1819 / Net I/σ(I): 5.046
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 13 Å / % possible obs: 93.5 % / Rmerge(I) obs: 0.112

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1fuo

1fuo


Resolution: 2.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1034 4.9 %Random
Rwork0.179 ---
all0.179 25744 --
obs0.179 21262 --
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6907 0 35 18 6960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d21.057
X-RAY DIFFRACTIONx_improper_angle_d1.269
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.261
LS refinement shellResolution: 2.6→2.71 Å /
RfactorNum. reflection
Rfree0.329 42
Rwork0.235 -
obs-765
Refinement
*PLUS
Highest resolution: 2.6 Å / Rfactor all: 0.179 / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.057
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.269
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / Rfactor Rwork: 0.235

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