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- PDB-5upp: Crystal structure of human fumarate hydratase -

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Basic information

Entry
Database: PDB / ID: 5upp
TitleCrystal structure of human fumarate hydratase
ComponentsFumarate hydratase, mitochondrial
KeywordsLYASE / HsFH / fumarase
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 / Mitochondrial protein degradation / chromosome / positive regulation of cold-induced thermogenesis / site of double-strand break / histone binding / mitochondrial matrix / DNA repair / DNA damage response / mitochondrion / extracellular exosome / nucleus / cytoplasm / cytosol
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: 1.8 Å
AuthorsRangel, V.L. / Ajalla, M.A. / Rustiguel, J.K. / Pereira de Padua, R.A. / Nonato, M.C.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/25075-0 Brazil
CAPES Brazil
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: Febs J. / Year: 2019
Title: Structural, biochemical and biophysical characterization of recombinant human fumarate hydratase.
Authors: Ajalla Aleixo, M.A. / Rangel, V.L. / Rustiguel, J.K. / de Padua, R.A.P. / Nonato, M.C.
History
DepositionFeb 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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)100,7554
Polymers100,2792
Non-polymers4772
Water15,547863
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)201,5118
Polymers200,5584
Non-polymers9534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area30040 Å2
ΔGint-181 kcal/mol
Surface area55920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.434, 148.006, 129.761
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-920-

HOH

21A-1029-

HOH

31A-1069-

HOH

41A-1096-

HOH

51A-1122-

HOH

61B-897-

HOH

71B-1019-

HOH

81B-1075-

HOH

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Components

#1: Protein Fumarate hydratase, mitochondrial / Fumarase


Mass: 50139.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FH / Plasmid: pET28a / 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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 863 / 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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5 1% (v/v) MPD 4% (w/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: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2016
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→48.79 Å / Num. obs: 111411 / % possible obs: 100 % / Redundancy: 5.3 % / Biso Wilson estimate: 23.27 Å2 / Rpim(I) all: 0.064 / Rrim(I) all: 0.151 / Rsym value: 0.137 / Net I/av σ(I): 3.2 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.8-1.95.30.6691.10.3210.7430.669100
1.9-2.015.30.4621.50.220.5130.462100
2.01-2.155.30.2972.30.140.3290.297100
2.15-2.325.20.2252.40.1060.2490.225100
2.32-2.555.20.1833.50.0850.2020.183100
2.55-2.855.50.15340.070.1690.153100
2.85-3.295.20.1324.70.0610.1460.132100
3.29-4.025.30.1135.10.0520.1250.113100
4.02-5.695.20.0985.60.0440.1070.098100
5.69-48.7865.10.0560.0250.0560.0599.9

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.6.0phasing
PHENIX1.11.1-2575-000refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D6B

5d6b


Resolution: 1.8→47.846 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.65
RfactorNum. reflection% reflection
Rfree0.1895 5565 5.03 %
Rwork0.1561 --
obs0.1578 110735 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.64 Å2 / Biso mean: 34.1841 Å2 / Biso min: 15.08 Å2
Refinement stepCycle: final / Resolution: 1.8→47.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6904 0 64 866 7834
Biso mean--67.95 40.55 -
Num. residues----924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087191
X-RAY DIFFRACTIONf_angle_d0.8719782
X-RAY DIFFRACTIONf_chiral_restr0.051131
X-RAY DIFFRACTIONf_plane_restr0.0071276
X-RAY DIFFRACTIONf_dihedral_angle_d10.9244419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.28881770.27663464364199
1.8205-1.84190.26771750.26963449362499
1.8419-1.86430.312020.2513429363199
1.8643-1.88790.28581840.24973399358398
1.8879-1.91280.26481890.23973466365599
1.9128-1.9390.28731710.24093492366399
1.939-1.96670.26062250.22453412363799
1.9667-1.99610.23121820.20513480366299
1.9961-2.02720.21091720.18693511368399
2.0272-2.06050.22571760.18333460363699
2.0605-2.0960.23052050.18373451365699
2.096-2.13410.20031800.16635033683100
2.1341-2.17520.21821650.157935003665100
2.1752-2.21960.19651840.15823487367199
2.2196-2.26780.18111670.15583515368299
2.2678-2.32060.18422070.14534873694100
2.3206-2.37860.22851430.144935543697100
2.3786-2.44290.1911860.141834793665100
2.4429-2.51480.18941830.140634983681100
2.5148-2.5960.16791940.141435093703100
2.596-2.68880.16251940.133935253719100
2.6888-2.79640.18121980.136935053703100
2.7964-2.92360.18631690.138835353704100
2.9236-3.07780.16231830.143735403723100
3.0778-3.27050.18541700.150235363706100
3.2705-3.5230.17521820.148535743756100
3.523-3.87740.19831970.137735553752100
3.8774-4.43810.13072030.119635683771100
4.4381-5.59020.15192030.13435983801100
5.5902-47.86260.20371990.18023689388899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.78460.4597-0.94172.9366-1.10521.99760.08680.0599-0.2366-0.1575-0.06470.17170.2094-0.1478-0.01010.2314-0.0353-0.06110.188-0.00810.2882-15.8407-88.7483-22.4494
21.28890.5872-0.22460.8967-0.16910.21130.1219-0.1839-0.1890.1579-0.1213-0.11620.00160.0205-0.00290.261-0.0298-0.0540.22970.02160.18955.7064-71.1767-15.7896
31.42850.2659-0.3140.6947-0.1640.2770.0639-0.0544-0.13440.0778-0.0712-0.06110.02410.05170.04220.2323-0.0227-0.04680.1790.00750.15222.0674-69.8208-21.3711
42.70090.64960.09361.29330.03720.53670.0484-0.12150.31690.0636-0.0306-0.5471-0.10660.164-0.02270.271-0.0393-0.08140.3240.02050.543543.1548-49.0648-20.399
51.79810.29360.55553.12751.17242.48570.1247-0.04970.2711-0.0995-0.063-0.1452-0.3030.0891-0.03530.2139-0.04390.0210.1674-0.01230.274715.6469-28.9936-22.2098
61.33510.38810.00950.62250.03070.18440.1071-0.15890.10790.1478-0.0732-0.006-0.06450.0566-0.03660.2403-0.0332-0.00380.1876-0.01070.1278-0.5936-47.9279-15.1175
76.9914-2.86212.7511.5597-0.3168.5265-0.1440.22110.72140.0324-0.15160.151-0.7823-0.07190.19330.24060.0288-0.00040.211-0.01530.348-31.6996-45.1782-31.9977
81.74320.1563-0.19710.79060.01690.26990.0437-0.0388-0.07210.1063-0.06310.30670.0128-0.11380.01360.2135-0.02090.01120.2053-0.02130.2054-25.1246-59.9628-22.934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 164 )A49 - 164
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 265 )A165 - 265
3X-RAY DIFFRACTION3chain 'A' and (resid 266 through 433 )A266 - 433
4X-RAY DIFFRACTION4chain 'A' and (resid 434 through 510 )A434 - 510
5X-RAY DIFFRACTION5chain 'B' and (resid 49 through 165 )B49 - 165
6X-RAY DIFFRACTION6chain 'B' and (resid 166 through 345 )B166 - 345
7X-RAY DIFFRACTION7chain 'B' and (resid 346 through 374 )B346 - 374
8X-RAY DIFFRACTION8chain 'B' and (resid 375 through 510 )B375 - 510

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