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- PDB-6ebt: Crystal structure of recombinant mutant N107T of human fumarase -

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Basic information

Entry
Database: PDB / ID: 6ebt
TitleCrystal structure of recombinant mutant N107T of human fumarase
ComponentsFumarate hydratase, mitochondrialFumarase
KeywordsLYASE / HsFH / fumarate hydratase
Function / homology
Function and homology information


regulation of arginine metabolic process / tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / Citric acid cycle (TCA cycle) / malate metabolic process / urea cycle / positive regulation of double-strand break repair via nonhomologous end joining / homeostasis of number of cells within a tissue ...regulation of arginine metabolic process / tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / Citric acid cycle (TCA cycle) / malate metabolic process / urea cycle / positive regulation of double-strand break repair via nonhomologous end joining / homeostasis of number of cells within a tissue / tricarboxylic acid cycle / site of double-strand break / chromosome / positive regulation of cold-induced thermogenesis / histone binding / mitochondrial matrix / DNA repair / DNA damage response / mitochondrion / extracellular exosome / nucleus / cytosol / 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAjalla, M.A.A. / Nonato, M.C.
CitationJournal: To Be Published
Title: Crystal structure of recombinant mutant N107T of human fumarase
Authors: Ajalla, M.A.A. / Nonato, M.C.
History
DepositionAug 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fumarate hydratase, mitochondrial
B: Fumarate hydratase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7137
Polymers100,2532
Non-polymers4605
Water8,791488
1
A: Fumarate hydratase, mitochondrial
B: Fumarate hydratase, mitochondrial
hetero molecules

A: Fumarate hydratase, mitochondrial
B: Fumarate hydratase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,42714
Polymers200,5064
Non-polymers92110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area31150 Å2
ΔGint-187 kcal/mol
Surface area54210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.816, 188.816, 114.145
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-788-

HOH

21A-865-

HOH

31A-899-

HOH

41A-915-

HOH

51A-929-

HOH

61B-743-

HOH

71B-844-

HOH

81B-876-

HOH

91B-932-

HOH

101B-935-

HOH

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Components

#1: Protein Fumarate hydratase, mitochondrial / Fumarase / Fumarase


Mass: 50126.395 Da / Num. of mol.: 2 / Mutation: N107T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FH / Plasmid: pET28a-SUMO / Details (production host): pET28a modified vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07954, fumarate hydratase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M HEPES 16% (m/v) PEG 10000 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2018
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→94.1 Å / Num. obs: 53547 / % possible obs: 100 % / Redundancy: 12.8 % / Net I/σ(I): 12.4
Reflection shellResolution: 2.3→2.37 Å

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.11.1-2575-000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UPP

5upp


Resolution: 2.3→93.597 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.38
RfactorNum. reflection% reflection
Rfree0.1854 2656 4.97 %
Rwork0.1502 --
obs0.152 53492 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→93.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6883 0 30 488 7401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027084
X-RAY DIFFRACTIONf_angle_d0.5269619
X-RAY DIFFRACTIONf_dihedral_angle_d9.4984278
X-RAY DIFFRACTIONf_chiral_restr0.0391117
X-RAY DIFFRACTIONf_plane_restr0.0031260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.34180.26451260.20342625X-RAY DIFFRACTION100
2.3418-2.38690.21061410.18872641X-RAY DIFFRACTION100
2.3869-2.43560.26451360.18142624X-RAY DIFFRACTION100
2.4356-2.48860.25181470.17972635X-RAY DIFFRACTION100
2.4886-2.54650.24251580.17142619X-RAY DIFFRACTION100
2.5465-2.61020.21161520.15982604X-RAY DIFFRACTION100
2.6102-2.68070.19461200.14842669X-RAY DIFFRACTION100
2.6807-2.75960.20191590.14772627X-RAY DIFFRACTION100
2.7596-2.84870.19961350.14662655X-RAY DIFFRACTION100
2.8487-2.95050.20621270.14492668X-RAY DIFFRACTION100
2.9505-3.06870.17811300.14892670X-RAY DIFFRACTION100
3.0687-3.20830.20381230.14042681X-RAY DIFFRACTION100
3.2083-3.37750.16031350.14192664X-RAY DIFFRACTION100
3.3775-3.58910.1841450.13372672X-RAY DIFFRACTION100
3.5891-3.86620.15671370.13142696X-RAY DIFFRACTION100
3.8662-4.25530.14321360.11672704X-RAY DIFFRACTION100
4.2553-4.8710.13791510.11542711X-RAY DIFFRACTION100
4.871-6.13680.1781290.1682778X-RAY DIFFRACTION100
6.1368-93.67440.17741690.18622893X-RAY DIFFRACTION100

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