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- PDB-6v8f: Crystal structure of recombinat mutant Q185R of human fumarase -

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Basic information

Entry
Database: PDB / ID: 6v8f
TitleCrystal structure of recombinat mutant Q185R 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 / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like
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.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development Brazil
CitationJournal: To Be Published
Title: Crystal structure of recombinat mutant Q185R of human fumarase
Authors: Ajalla, M.A.A. / Nonato, M.C.
History
DepositionDec 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: 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)100,7848
Polymers100,3372
Non-polymers4476
Water10,863603
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)201,56816
Polymers200,6744
Non-polymers89412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area30840 Å2
ΔGint-262 kcal/mol
Surface area55700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.489, 190.489, 115.184
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-736-

HOH

21A-841-

HOH

31A-925-

HOH

41A-963-

HOH

51A-992-

HOH

61B-779-

HOH

71B-928-

HOH

81B-945-

HOH

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Components

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


Mass: 50168.457 Da / Num. of mol.: 2 / Mutation: Q185R
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 BL21(DE3) (bacteria) / References: UniProt: P07954, fumarate hydratase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 0.2 M Lithium sulfate, 25% (m/v) PEG 3350
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2018
RadiationMonochromator: channel cut cryogenically cooled monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.3→95.244 Å / Num. obs: 54953 / % possible obs: 100 % / Redundancy: 32.4 % / CC1/2: 0.999 / Net I/σ(I): 19.6
Reflection shellResolution: 2.3→2.37 Å / Num. unique obs: 4425 / CC1/2: 0.927

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UPP

5upp


Resolution: 2.3→95.24 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 14.98
RfactorNum. reflection% reflection
Rfree0.1811 2724 4.96 %
Rwork0.1502 --
obs0.1518 54896 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.65 Å2 / Biso mean: 34.1849 Å2 / Biso min: 7.83 Å2
Refinement stepCycle: final / Resolution: 2.3→95.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6877 0 24 603 7504
Biso mean--69.56 38.71 -
Num. residues----924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.34180.21541360.20722711100
2.3418-2.38690.28041270.19952691100
2.3869-2.43560.23461390.18562700100
2.4356-2.48860.21581270.18672712100
2.4886-2.54650.23171560.17562703100
2.5465-2.61010.18261550.17282700100
2.6101-2.68070.20861400.16362729100
2.6807-2.75960.18751460.15712695100
2.7596-2.84870.20041530.16722702100
2.8487-2.95050.20421430.1582732100
2.9505-3.06860.20541450.16142710100
3.0686-3.20830.19311560.16072740100
3.2083-3.37750.19981370.16182738100
3.3775-3.58910.1761570.14462745100
3.5891-3.86620.15281430.12522751100
3.8662-4.25530.15861420.1182778100
4.2553-4.8710.13721470.11372796100
4.871-6.13680.18291280.14892853100
6.1368-95.240.14211470.1431298699

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