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- PDB-6msn: Crystal structure of cytosolic fumarate hydratase from Leishmania... -

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Basic information

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


fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / glycosome / ciliary plasm / generation of precursor metabolites and energy / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding ...fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / glycosome / ciliary plasm / generation of precursor metabolites and energy / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding / cytosol / 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
Similarity search - Domain/homology
(2S)-2-sulfanylbutanedioic acid / IRON/SULFUR CLUSTER / Fumarate hydratase 2
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.591 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,0316
Polymers133,0272
Non-polymers1,0044
Water14,790821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-78 kcal/mol
Surface area33960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.727, 84.680, 239.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein fumarate hydratase / Fumarase


Mass: 66513.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_29_1960 / Production host: Escherichia coli (E. coli) / References: UniProt: E9AE57, fumarate hydratase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-JYD / (2S)-2-sulfanylbutanedioic acid / thiomalate / Thiomalic acid


Mass: 150.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 821 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 12 % PEG 3,350, 10 mM ammonium citrate tribasic, 16 mM sodium acetate trihydrate, 20 mM sodium formate, 6.4 mM ammonium tartrate dibasic, 12 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, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 178641 / % possible obs: 99.8 % / Redundancy: 5.4 % / Rsym value: 0.135 / Net I/σ(I): 10.16
Reflection shellResolution: 1.59→1.63 Å / Redundancy: 4.8 % / CC1/2: 0.642 / Rsym value: 0.8 / % possible all: 99.5

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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: 1.591→48.955 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.91
RfactorNum. reflection% reflection
Rfree0.1699 8927 5 %
Rwork0.153 --
obs0.1539 178532 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.591→48.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8147 0 34 821 9002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048956
X-RAY DIFFRACTIONf_angle_d0.71712237
X-RAY DIFFRACTIONf_dihedral_angle_d7.3527935
X-RAY DIFFRACTIONf_chiral_restr0.051314
X-RAY DIFFRACTIONf_plane_restr0.0051624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5913-1.60940.29722410.26564567X-RAY DIFFRACTION81
1.6094-1.62830.25632940.25115612X-RAY DIFFRACTION100
1.6283-1.64820.24892960.23115613X-RAY DIFFRACTION100
1.6482-1.66910.25062940.2145598X-RAY DIFFRACTION100
1.6691-1.6910.22462970.20535618X-RAY DIFFRACTION100
1.691-1.71420.21452960.20335635X-RAY DIFFRACTION100
1.7142-1.73870.21182970.19075641X-RAY DIFFRACTION100
1.7387-1.76460.19152970.17765651X-RAY DIFFRACTION100
1.7646-1.79220.21012970.17125636X-RAY DIFFRACTION100
1.7922-1.82160.19512980.16675658X-RAY DIFFRACTION100
1.8216-1.8530.21092960.1685630X-RAY DIFFRACTION100
1.853-1.88670.20012990.17155677X-RAY DIFFRACTION100
1.8867-1.9230.17312970.15515632X-RAY DIFFRACTION100
1.923-1.96220.17782960.15075634X-RAY DIFFRACTION100
1.9622-2.00490.16342990.14645697X-RAY DIFFRACTION100
2.0049-2.05160.17052980.14395657X-RAY DIFFRACTION100
2.0516-2.10290.15572980.1395656X-RAY DIFFRACTION100
2.1029-2.15970.1472960.13935638X-RAY DIFFRACTION100
2.1597-2.22330.14933020.13745714X-RAY DIFFRACTION100
2.2233-2.2950.1622990.14235695X-RAY DIFFRACTION100
2.295-2.3770.17712990.14345675X-RAY DIFFRACTION100
2.377-2.47220.16623010.14585703X-RAY DIFFRACTION100
2.4722-2.58470.17092970.14565660X-RAY DIFFRACTION100
2.5847-2.7210.18613020.14865725X-RAY DIFFRACTION100
2.721-2.89150.16013020.15115752X-RAY DIFFRACTION100
2.8915-3.11470.17513020.14415740X-RAY DIFFRACTION100
3.1147-3.4280.15173040.14365774X-RAY DIFFRACTION100
3.428-3.92390.1443050.13535783X-RAY DIFFRACTION100
3.9239-4.9430.12093080.12695858X-RAY DIFFRACTION100
4.943-48.9780.1813200.16736076X-RAY DIFFRACTION99
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)
10.29670.00470.05360.5347-0.14320.5654-0.0021-0.07240.00160.0945-0.0453-0.0679-0.08490.06940.05330.1164-0.008-0.03250.10750.01080.111934.34990.6679-22.3504
20.3990.03830.03260.4221-0.11480.5532-0.0341-0.0054-0.0185-0.0121-0.0055-0.0783-0.05850.06730.03740.087-0.0011-0.00390.09750.0170.101233.009-10.1704-35.2048
30.80140.00560.09911.2872-0.2980.98730.03480.0480.0975-0.02820.00190.1197-0.0746-0.0698-0.03650.1558-0.0012-0.03110.09760.02470.146720.203416.99-45.1631
41.0198-0.15940.19191.3887-0.01090.80150.0234-0.2491-0.09780.2131-0.0141-0.03250.0218-0.0485-0.00660.143-0.01750.00630.1730.04140.088819.6999-22.3798-7.1764
52.8606-0.04931.10550.68890.50461.49760.0035-0.1455-0.02660.1046-0.10370.26450.0985-0.33880.08460.1069-0.05210.03280.2101-0.00210.1732-2.7616-32.2709-27.2106
61.35821.41151.15872.61341.4842.01960.0736-0.1668-0.0740.1804-0.0937-0.04610.1096-0.07260.01440.08060.00620.01030.10370.02840.084620.9926-28.2324-17.5122
70.27250.32410.37770.64030.15372.95380.0479-0.0443-0.10060.0515-0.0242-0.11070.17210.0549-0.00380.08760.0318-0.0070.09840.02630.145228.0703-33.3562-26.7919
80.48210.10840.07590.58250.16210.5636-0.0023-0.03030.04750.0099-0.03160.132-0.0462-0.11830.03590.0770.01460.00230.1234-0.00520.11699.0448-13.6961-27.4843
90.80330.42330.66950.4930.36661.10340.0866-0.1325-0.11310.0544-0.07490.09470.3046-0.37370.0010.139-0.0231-0.00860.13570.01310.19312.6042-38.9874-36.0319
100.837-0.14330.2061.1317-0.17781.60340.03560.0436-0.1017-0.0933-0.0370.03970.1646-0.060.00550.1145-0.0116-0.01170.0766-0.01330.116212.2875-37.9685-47.0415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 194 )
2X-RAY DIFFRACTION2chain 'A' and (resid 195 through 369 )
3X-RAY DIFFRACTION3chain 'A' and (resid 370 through 568 )
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 87 )
5X-RAY DIFFRACTION5chain 'B' and (resid 88 through 127 )
6X-RAY DIFFRACTION6chain 'B' and (resid 128 through 154 )
7X-RAY DIFFRACTION7chain 'B' and (resid 155 through 194 )
8X-RAY DIFFRACTION8chain 'B' and (resid 195 through 357 )
9X-RAY DIFFRACTION9chain 'B' and (resid 358 through 409 )
10X-RAY DIFFRACTION10chain 'B' and (resid 410 through 568 )

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