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- PDB-6vbe: Crystal structure of recombinant mutant H180R of human fumarase -

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Basic information

Entry
Database: PDB / ID: 6vbe
TitleCrystal structure of recombinant mutant H180R 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
L(+)-TARTARIC ACID / Fumarate hydratase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsAjalla, M.A.A. / Nonato, M.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Coordination for the Improvement of Higher Education Personnel Brazil
CitationJournal: To Be Published
Title: Crystal structure of recombinant mutant H180R of human fumarase
Authors: Ajalla, M.A.A. / Notato, M.C.
History
DepositionDec 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)100,7436
Polymers100,3172
Non-polymers4264
Water10,431579
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)201,48712
Polymers200,6344
Non-polymers8538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area32230 Å2
ΔGint-180 kcal/mol
Surface area54520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.880, 189.880, 115.380
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-848-

HOH

21A-910-

HOH

31A-928-

HOH

41B-725-

HOH

51B-866-

HOH

61B-915-

HOH

71B-944-

HOH

81B-951-

HOH

91B-971-

HOH

101B-972-

HOH

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Components

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


Mass: 50158.441 Da / Num. of mol.: 2 / Mutation: H180R
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.86 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 294 K / Method: liquid diffusion / Details: 0.2 M Amonium tartrate dibasic, 14% (m/v) PEG 3350

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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: Oct 6, 2016
RadiationMonochromator: chanel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.899→49.302 Å / Num. obs: 182979 / % possible obs: 99.6 % / Redundancy: 22.3 % / CC1/2: 0.999 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 6844 / CC1/2: 0.338

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Processing

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

5upp


Resolution: 1.899→49.302 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.72
RfactorNum. reflection% reflection
Rfree0.1927 9163 5.01 %
Rwork0.1648 --
obs0.1662 182979 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.03 Å2 / Biso mean: 44.309 Å2 / Biso min: 23.1 Å2
Refinement stepCycle: final / Resolution: 1.899→49.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6901 0 28 579 7508
Biso mean--53.18 47.74 -
Num. residues----924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087134
X-RAY DIFFRACTIONf_angle_d0.8649687
X-RAY DIFFRACTIONf_dihedral_angle_d14.8172616
X-RAY DIFFRACTIONf_chiral_restr0.0521125
X-RAY DIFFRACTIONf_plane_restr0.0061268
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.899-1.92010.45142880.4346547794
1.9201-1.94270.40423020.38675787100
1.9427-1.96640.38063030.3481583199
1.9664-1.99130.35613050.3196573899
1.9913-2.01750.35753100.2935820100
2.0175-2.04510.28923040.27925761100
2.0451-2.07430.30293020.2766577299
2.0743-2.10530.28793030.2683581599
2.1053-2.13820.28023040.2605581499
2.1382-2.17330.26873080.25225750100
2.1733-2.21070.23743100.21255811100
2.2107-2.25090.22163040.19765806100
2.2509-2.29420.22213040.18895816100
2.2942-2.34110.19853060.18155798100
2.3411-2.3920.22223050.17945809100
2.392-2.44760.21623040.17345777100
2.4476-2.50880.22043060.17755827100
2.5088-2.57660.23783060.17645792100
2.5766-2.65250.22053070.16875807100
2.6525-2.73810.20273060.15815839100
2.7381-2.83590.21362970.15955800100
2.8359-2.94940.2013100.15145820100
2.9494-3.08370.1763120.15085832100
3.0837-3.24620.17233060.15175788100
3.2462-3.44950.19153070.15295822100
3.4495-3.71580.16263090.14375830100
3.7158-4.08960.16293110.12425814100
4.0896-4.6810.13693120.11645800100
4.681-5.8960.1593120.14625834100
5.896-49.3020.13623000.13955829100

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