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- PDB-1fur: FUMARASE MUTANT H188N WITH BOUND SUBSTRATE L-MALATE AT PUTATIVE A... -

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Basic information

Entry
Database: PDB / ID: 1fur
TitleFUMARASE MUTANT H188N WITH BOUND SUBSTRATE L-MALATE AT PUTATIVE ACTIVATOR SITE
ComponentsFUMARASE C
KeywordsHYDROLYASE / CARBON OXYGEN LYASE / KREB'S CYCLE ENZYME / FUMARATE HYDRATASE
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
D-MALATE / Fumarate hydratase class II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWeaver, T.M. / Lees, M. / Banaszak, L.J.
CitationJournal: Protein Sci. / Year: 1997
Title: Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site.
Authors: Weaver, T. / Lees, M. / Banaszak, L.
History
DepositionJan 9, 1997Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FUMARASE C
B: FUMARASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3184
Polymers101,0492
Non-polymers2682
Water7,242402
1
A: FUMARASE C
B: FUMARASE C
hetero molecules

A: FUMARASE C
B: FUMARASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,6358
Polymers202,0994
Non-polymers5364
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Buried area28610 Å2
ΔGint-197 kcal/mol
Surface area54510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.030, 219.320, 86.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.497147, -0.009049, 0.867619), (-0.017876, -0.99984, -0.000185), (0.867482, -0.015418, -0.49723)
Vector: -2.89074, 282.67993, 9.29937)

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Components

#1: Protein FUMARASE C / FUMC


Mass: 50524.727 Da / Num. of mol.: 2 / Mutation: H188N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM105
Description: SITE-DIRECTED MUTANT OF FUMARASE C WAS GENERATED BY PCR. THE NATIVE ENZYME ALSO INCORPORATES A 5 HIS TAG ON THE CARBOXY TERMINUS THAT IS NOT VISIBLE IN THE ELECTRON DENSITY MAPS ...Description: SITE-DIRECTED MUTANT OF FUMARASE C WAS GENERATED BY PCR. THE NATIVE ENZYME ALSO INCORPORATES A 5 HIS TAG ON THE CARBOXY TERMINUS THAT IS NOT VISIBLE IN THE ELECTRON DENSITY MAPS CALCULATED USING PHASES CALCULATED FROM THE FINAL MODEL COORDINATES.
Cell line: 293 / Cellular location: CYTOPLASM / Gene: FUMC / Plasmid: PASK40_188EFUMC / Cellular location (production host): CYTOPLASM / Gene (production host): FUMC / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / 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.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 %
Crystal growpH: 5
Details: PROTEIN WAS CRYSTALLIZED FROM 150MM CITRATE PH 5.0 AND 14% PEG 4000
Crystal grow
*PLUS
pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1300 mMcitrate11
212-14 %(w/v)PEG335011

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→8 Å / Num. obs: 79307 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.064 / Rsym value: 0.094 / Net I/σ(I): 10.2
Reflection shellResolution: 1.81→1.88 Å / Redundancy: 0.75 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 0.55 / Rsym value: 0.38 / % possible all: 49
Reflection shell
*PLUS
% possible obs: 75 %

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Processing

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

1fuo


Resolution: 1.95→8 Å / Rfactor Rfree error: 0.0025 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.209 7021 9.7 %RANDOM
Rwork0.17 ---
obs0.17 72286 87.6 %-
Refinement stepCycle: LAST / Resolution: 1.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6907 0 18 402 7327
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_deg1.26
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3LMAL.PARLMAL.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / 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_deg21.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.25

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