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- PDB-2fus: MUTATIONS OF FUMARASE THAT DISTINGUISH BETWEEN THE ACTIVE SITE AN... -

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Basic information

Entry
Database: PDB / ID: 2fus
TitleMUTATIONS OF FUMARASE THAT DISTINGUISH BETWEEN THE ACTIVE SITE AND A NEARBY DICARBOXYLIC ACID BINDING SITE
ComponentsFUMARASE C
KeywordsHYDROLYASE / CARBON OXYGEN LYASE / KREB'S CYCLE ENZYME / FUMARATE HYDRATASE
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) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) ...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 / Fumarase/aspartase (N-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / 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 / Fumarate hydratase class II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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
Revision 1.5May 29, 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 C
B: FUMARASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4344
Polymers101,0492
Non-polymers3842
Water6,684371
1
A: FUMARASE C
B: FUMARASE C
hetero molecules

A: FUMARASE C
B: FUMARASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,8678
Polymers202,0994
Non-polymers7684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Buried area29540 Å2
ΔGint-193 kcal/mol
Surface area54180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.160, 220.050, 86.650
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: (0.4695, -0.0031, 0.8829), (-0.004, -1, -0.0014), (0.8829, -0.0029, -0.4695)
Vector: -1.8982, 282.04489, 4.1551)

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Components

#1: Protein FUMARASE C / FUMC


Mass: 50524.730 Da / Num. of mol.: 2 / Mutation: H129N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM105 / Cell line: 293 / Cellular location: CYTOPLASM / Gene: FUMC / Plasmid: PASK40_129EFUMC / Cellular location (production host): CYTOPLASM / Gene (production host): FUMC / Production host: Escherichia coli (E. coli) / References: UniProt: P05042, fumarate hydratase
#2: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SECOND ANION BINDING SITE LOCATED BETWEEN ARG 126 THROUGH ASN 135 HAS BEEN STERICALLY BLOCKED ...THE SECOND ANION BINDING SITE LOCATED BETWEEN ARG 126 THROUGH ASN 135 HAS BEEN STERICALLY BLOCKED BY THE MUTATION OF HIS 129 - AN ASN. THE OD1 ATOM OF ASN 129 BLOCKS THIS SITE BY FORMING A BIFURCATED HYDROGEN BOND TO THE AMIDE NITROGENS OF ASP 132 AND ASN 131.

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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: Feb 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→8 Å / Num. obs: 60762 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Rsym value: 0.117 / Net I/σ(I): 7.4
Reflection shellResolution: 1.98→2.06 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 0.435 / Rsym value: 0.71 / % possible all: 46
Reflection shell
*PLUS
% possible obs: 46 %

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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: 2.2→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4890 8.75 %RANDOM
Rwork0.178 ---
obs0.178 55872 87.8 %-
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6907 0 26 371 7304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.28
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
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: 2.2→2.3 Å / Total num. of bins used: 8 / % reflection obs: 85.26 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH.WAT
X-RAY DIFFRACTION3CIT.PARCIT.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_deg21.25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29

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