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- PDB-6mso: Crystal structure of mitochondrial fumarate hydratase from Leishm... -

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Basic information

Entry
Database: PDB / ID: 6mso
TitleCrystal structure of mitochondrial fumarate hydratase from Leishmania major in a complex with inhibitor thiomalate
Componentsfumarate hydrataseFumarase
KeywordsLYASE/LYASE inhibitor / inhibitor / mitochondrial / fumarate hydratase / LYASE / LYASE-LYASE inhibitor complex
Function / homology
Function and homology information


fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / tricarboxylic acid cycle / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
Iron-dependent fumarate hydratase / Fe-S hydro-lyase, tartrate dehydratase alpha-type, catalytic domain / Fumarate hydratase (Fumerase) / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain superfamily / Fumarase C-terminus / Fumarate lyase, conserved site / Fumarate lyases signature.
Similarity search - Domain/homology
(2S)-2-sulfanylbutanedioic acid / IRON/SULFUR CLUSTER / Fumarate hydratase 1, mitochondrial
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.053 Å
AuthorsFeliciano, P.R. / Drennan, C.L. / Nonato, M.C.
Funding support Brazil, United States, 5items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/22246-4 Brazil
Sao Paulo Research Foundation (FAPESP)2013/14988-8 Brazil
Sao Paulo Research Foundation (FAPESP)2008/08262-6 Brazil
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: ACS Chem. Biol. / Year: 2019
Title: Crystal Structures of Fumarate Hydratases from Leishmania major in a Complex with Inhibitor 2-Thiomalate.
Authors: Feliciano, P.R. / Drennan, C.L. / Nonato, M.C.
History
DepositionOct 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: fumarate hydratase
B: fumarate hydratase
C: fumarate hydratase
D: fumarate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,98030
Polymers258,8534
Non-polymers5,12726
Water15,619867
1
A: fumarate hydratase
B: fumarate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,50419
Polymers129,4262
Non-polymers3,07817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11980 Å2
ΔGint-58 kcal/mol
Surface area36250 Å2
MethodPISA
2
C: fumarate hydratase
D: fumarate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,47511
Polymers129,4262
Non-polymers2,0499
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-77 kcal/mol
Surface area35830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.741, 138.443, 138.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
fumarate hydratase / Fumarase


Mass: 64713.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_24_0320 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QAU9, fumarate hydratase

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Non-polymers , 5 types, 893 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-JYD / (2S)-2-sulfanylbutanedioic acid / thiomalate / Thiomalic acid


Mass: 150.153 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 867 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 2.2 M ammonium sulfate, 4 % PEG 400, 10 mM RS-thiomalate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 180831 / % possible obs: 98.6 % / Redundancy: 6.3 % / Rsym value: 0.15 / Net I/σ(I): 9.75
Reflection shellResolution: 2.05→2.09 Å / Mean I/σ(I) obs: 1.33 / CC1/2: 0.706 / Rsym value: 0.605

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L2R

5l2r


Resolution: 2.053→48.881 Å / Cross valid method: FREE R-VALUE / σ(F): 186.13 / Phase error: 20.15
RfactorNum. reflection% reflection
Rfree0.2045 9156 5.06 %
Rwork0.1594 --
obs0.1668 180803 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.053→48.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16335 0 222 867 17424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817039
X-RAY DIFFRACTIONf_angle_d1.02123051
X-RAY DIFFRACTIONf_dihedral_angle_d8.67514135
X-RAY DIFFRACTIONf_chiral_restr0.0572510
X-RAY DIFFRACTIONf_plane_restr0.0073000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0542-2.08960.23884180.20397778X-RAY DIFFRACTION84
2.0896-2.12760.23464460.19768439X-RAY DIFFRACTION92
2.1276-2.16860.23154410.19138473X-RAY DIFFRACTION93
2.1686-2.21280.23074480.18948552X-RAY DIFFRACTION94
2.2128-2.26090.22124440.18458692X-RAY DIFFRACTION94
2.2609-2.31350.21714520.17558606X-RAY DIFFRACTION94
2.3135-2.37140.2244490.17928468X-RAY DIFFRACTION93
2.3714-2.43550.21774580.17258606X-RAY DIFFRACTION94
2.4355-2.50720.21364500.17368681X-RAY DIFFRACTION95
2.5072-2.58810.22084670.17118620X-RAY DIFFRACTION94
2.5881-2.68060.2514430.16988644X-RAY DIFFRACTION94
2.6806-2.78790.20144540.16938692X-RAY DIFFRACTION94
2.7879-2.91480.22844680.16168718X-RAY DIFFRACTION94
2.9148-3.06840.2194520.15928461X-RAY DIFFRACTION92
3.0684-3.26060.21354540.15828687X-RAY DIFFRACTION95
3.2606-3.51230.20464580.15758708X-RAY DIFFRACTION95
3.5123-3.86570.18294720.15728735X-RAY DIFFRACTION95
3.8657-4.42470.20114550.14188637X-RAY DIFFRACTION94
4.4247-5.57340.16664640.14498721X-RAY DIFFRACTION94
5.5734-48.89530.20324640.17568780X-RAY DIFFRACTION94
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)
11.27290.034-0.97510.626-0.82333.40080.0258-0.14670.16860.1484-0.02620.1109-0.21740.0223-0.00170.11490.02410.03050.1259-0.07990.369299.202224.514178.2441
20.73880.0218-0.07290.1624-0.03230.21460.0035-0.03740.03610.0803-0.01250.1146-0.0655-0.0414-0.0021-0.03530.0185-0.00780.1227-0.02340.342196.55934.272868.5161
30.35520.12070.07650.052-0.00160.0988-0.02040.02990.06440.004-0.00690.1009-0.0333-0.1209-0.01720.00140.020.00140.16320.00190.379391.29366.682861.413
40.7875-0.044-0.00260.22520.17410.50360.0506-0.0111-0.15540.0094-0.07190.21750.0609-0.08750.00910.0885-0.02-0.01070.1353-0.00580.39391.4149-23.144966.7165
52.07781.7038-0.34831.6823-0.50150.22060.076-0.22270.14880.2294-0.09140.0848-0.09720.02460.01630.1225-0.0054-0.05830.1662-0.05710.2741119.633119.523282.5732
60.61960.0995-0.13210.0860.01440.2658-0.00810.05960.04520.0129-0.0099-0.0402-0.05630.0566-0.0013-0.0263-0.0112-0.01120.1308-0.00450.3453126.602917.530659.2817
70.5989-0.0732-0.01570.1825-0.02890.15590.0185-0.0049-0.03870.0264-0.02710.01080.00240.01790.00410.01880.0105-0.00560.1332-0.01280.3072116.19774.76562.5332
81.75360.0731-0.92760.13030.0510.9545-0.0199-0.0936-0.05140.01340.0034-0.06260.02460.09360.01540.03590.0121-0.02780.11840.00180.3009123.6928-1.901466.0341
90.85750.06530.03210.17960.02930.3674-0.03440.05660.07850.02190.06-0.0198-0.0510.08870.04560.01950.0036-0.03120.1163-0.0090.2861126.174610.903668.1285
101.93650.00360.41030.36190.20130.52320.03420.3818-0.0775-0.15370.0365-0.0772-0.01720.1829-0.05760.1246-0.00310.03590.3056-0.01360.2285127.23358.77935.1199
112.20931.54410.48264.02690.4720.885-0.0983-0.11150.0384-0.07980.06970.41140.1379-0.37380.03780.2169-0.07390.01190.51270.09870.212478.71975.2949148.8654
120.04320.1681-0.24491.4566-0.65921.5250.0443-0.0545-0.09840.0398-0.0804-0.00280.0864-0.03270.03120.1242-0.0391-0.00690.34780.04530.303375.80333.0865130.9796
130.36390.3470.3640.51240.23560.44410.0165-0.07720.05340.0368-0.06260.0032-0.0251-0.14970.04370.13830.03350.01920.3429-0.00720.314583.223419.1167134.3841
141.1046-0.15950.72920.31220.02670.5827-0.0481-0.11920.07280.08680.01910.2986-0.0573-0.18550.0270.14590.02160.05230.362-0.0250.329874.946219.3288133.9857
152.1194-0.2575-0.99480.71270.1910.890.09830.22390.0489-0.09950.04950.2173-0.0365-0.3496-0.13160.15610.0179-0.01870.35110.01740.315974.784212.4753103.4098
163.7394-0.4311-1.71262.9835-0.90571.4619-0.01590.07420.02470.01630.18930.2407-0.0122-0.2378-0.17490.13230.0121-0.07440.3933-0.02020.214373.609113.6481105.3018
171.78210.82552.36880.43981.1243.20770.1303-0.1735-0.23890.03740.0217-0.06820.3002-0.0786-0.13940.16650.0274-0.03130.33090.03720.3158104.212.6652148.7679
180.10430.3069-0.13371.0212-0.31881.2890.0092-0.01360.10160.05610.064-0.0842-0.02380.1341-0.07460.1021-0.0071-0.01420.30910.0150.3207106.508920.4028143.9323
193.71272.2941.46531.72890.57031.0228-0.01330.1469-0.066-0.05910.0036-0.1240.04150.17370.01830.1450.05560.05160.2721-0.01970.2556104.20715.5153123.0697
201.2880.19840.28141.05470.12270.4997-0.0851-0.0090.3842-0.02190.0117-0.1172-0.18610.2250.06610.1896-0.02270.02230.36110.02110.4128109.869334.7746137.9818
213.7784-0.80530.32261.7459-1.26832.09640.06490.37640.55040.0831-0.1701-0.2076-0.32840.26660.09420.1976-0.04410.0060.27090.01970.4837107.854744.2612134.4624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 279 )
3X-RAY DIFFRACTION3chain 'A' and (resid 280 through 355 )
4X-RAY DIFFRACTION4chain 'A' and (resid 356 through 549 )
5X-RAY DIFFRACTION5chain 'B' and (resid 10 through 52 )
6X-RAY DIFFRACTION6chain 'B' and (resid 53 through 165 )
7X-RAY DIFFRACTION7chain 'B' and (resid 166 through 228 )
8X-RAY DIFFRACTION8chain 'B' and (resid 229 through 312 )
9X-RAY DIFFRACTION9chain 'B' and (resid 313 through 355 )
10X-RAY DIFFRACTION10chain 'B' and (resid 356 through 549 )
11X-RAY DIFFRACTION11chain 'C' and (resid 12 through 39 )
12X-RAY DIFFRACTION12chain 'C' and (resid 40 through 165 )
13X-RAY DIFFRACTION13chain 'C' and (resid 166 through 279 )
14X-RAY DIFFRACTION14chain 'C' and (resid 280 through 351 )
15X-RAY DIFFRACTION15chain 'C' and (resid 352 through 478 )
16X-RAY DIFFRACTION16chain 'C' and (resid 479 through 548 )
17X-RAY DIFFRACTION17chain 'D' and (resid 12 through 69 )
18X-RAY DIFFRACTION18chain 'D' and (resid 70 through 201 )
19X-RAY DIFFRACTION19chain 'D' and (resid 202 through 312 )
20X-RAY DIFFRACTION20chain 'D' and (resid 313 through 451 )
21X-RAY DIFFRACTION21chain 'D' and (resid 452 through 548 )

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