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

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Basic information

Entry
Database: PDB / ID: 6uoi
TitleCrystal structure of cytosolic fumarate hydratase from Leishmania major in a complex with malonate
ComponentsFumarate hydratase 2Fumarase
KeywordsLYASE/LYASE INHIBITOR / fumarate hydratase / fumarase / Leishmania major / inhibitor / malonate / LYASE-LYASE INHIBITOR complex
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
FE3-S4 CLUSTER / : / MALONIC ACID / Fumarate hydratase 2
Similarity search - Component
Biological speciesLeishmania major strain Friedlin (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.953 Å
AuthorsFeliciano, P.R. / Drennan, C.L.
Funding support Brazil, United States, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/22246-4 Brazil
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structural and Biochemical Investigations of the [4Fe-4S] Cluster-Containing Fumarate Hydratase fromLeishmania major.
Authors: Feliciano, P.R. / Drennan, C.L.
History
DepositionOct 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: 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 1.2Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fumarate hydratase 2
B: Fumarate hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,44713
Polymers133,0272
Non-polymers1,42011
Water15,655869
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-141 kcal/mol
Surface area33920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.578, 85.102, 240.231
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 28 through 54 or (resid 55...
21(chain B and (resid 28 through 43 or (resid 44...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLUGLU(chain A and (resid 28 through 54 or (resid 55...AA28 - 5464 - 90
12LYSLYSLYSLYS(chain A and (resid 28 through 54 or (resid 55...AA5591
13ASNASNALAALA(chain A and (resid 28 through 54 or (resid 55...AA26 - 56862 - 604
14ASNASNALAALA(chain A and (resid 28 through 54 or (resid 55...AA26 - 56862 - 604
15ASNASNALAALA(chain A and (resid 28 through 54 or (resid 55...AA26 - 56862 - 604
16GLUGLUGLUGLU(chain A and (resid 28 through 54 or (resid 55...AA6197
17ASNASNALAALA(chain A and (resid 28 through 54 or (resid 55...AA26 - 56862 - 604
18ASNASNALAALA(chain A and (resid 28 through 54 or (resid 55...AA26 - 56862 - 604
19ASNASNALAALA(chain A and (resid 28 through 54 or (resid 55...AA26 - 56862 - 604
110ASNASNALAALA(chain A and (resid 28 through 54 or (resid 55...AA26 - 56862 - 604
111ASNASNALAALA(chain A and (resid 28 through 54 or (resid 55...AA26 - 56862 - 604
112ASNASNALAALA(chain A and (resid 28 through 54 or (resid 55...AA26 - 56862 - 604
113ASNASNALAALA(chain A and (resid 28 through 54 or (resid 55...AA26 - 56862 - 604
21ASPASPHISHIS(chain B and (resid 28 through 43 or (resid 44...BB28 - 4364 - 79
22GLNGLNGLNGLN(chain B and (resid 28 through 43 or (resid 44...BB4480
23ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
24ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
25ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
26ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
27ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604
28ASPASPALAALA(chain B and (resid 28 through 43 or (resid 44...BB28 - 56864 - 604

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fumarate hydratase 2 / Fumarase / LmFH-2


Mass: 66513.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major strain Friedlin (eukaryote)
Strain: Friedlin / Gene: FH2, LMJF_29_1960 / Production host: Escherichia coli (E. coli) / References: UniProt: E9AE57, fumarate hydratase

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Non-polymers , 5 types, 880 molecules

#2: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 869 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 12% v/v PEG3350, 10 mM ammonium citrate tribasic, 16 mM sodium acetate trihydrate, 20 mM sodium formate, 6.4 mM ammonium tartrate dibasic, 73.2 mM malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 98420 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.699 / Net I/σ(I): 12.2
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 98420 / CC1/2: 0.699

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5L2R

5l2r


Resolution: 1.953→49.069 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.88
RfactorNum. reflection% reflection
Rfree0.176 4916 5 %
Rwork0.1471 --
obs0.1486 98315 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.88 Å2 / Biso mean: 27.9842 Å2 / Biso min: 10.15 Å2
Refinement stepCycle: final / Resolution: 1.953→49.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8199 0 64 882 9145
Biso mean--25.8 37.91 -
Num. residues----1067
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2804X-RAY DIFFRACTION4.633TORSIONAL
12B2804X-RAY DIFFRACTION4.633TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.953-1.97480.26471560.2529297097
1.9748-1.9980.24511620.22883068100
1.998-2.02240.26611640.21873101100
2.0224-2.0480.26071610.2023064100
2.048-2.07490.22441620.20093089100
2.0749-2.10330.20931600.18573047100
2.1033-2.13340.23721630.17473093100
2.1334-2.16520.20751610.1653058100
2.1652-2.19910.18121640.15893113100
2.1991-2.23510.19861620.15523088100
2.2351-2.27360.20341620.15873065100
2.2736-2.3150.21371630.15953089100
2.315-2.35950.17081610.1533085100
2.3595-2.40770.20161640.15223110100
2.4077-2.460.20121630.15153084100
2.46-2.51720.17731640.14353113100
2.5172-2.58020.16941640.143107100
2.5802-2.650.18041630.13923104100
2.65-2.72790.19651630.13733099100
2.7279-2.8160.16261630.13783101100
2.816-2.91660.17591640.13653109100
2.9166-3.03340.17461650.13363135100
3.0334-3.17140.1541650.13763137100
3.1714-3.33860.14531640.13633127100
3.3386-3.54770.15681660.12693149100
3.5477-3.82150.15321660.12513154100
3.8215-4.20590.14371660.12313153100
4.2059-4.8140.12451680.1133203100
4.814-6.06340.17231700.15273216100
6.0634-49.0690.19531770.1749336899
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)
10.822-0.16240.06481.0090.05492.2368-0.0133-0.0926-0.01590.1942-0.0888-0.1967-0.19990.25220.09740.1748-0.0212-0.07030.21260.04570.219439.242234.2248106.6735
20.4840.12160.07060.6833-0.06470.7696-0.0520.00450.0564-0.043-0.0131-0.0516-0.21470.08290.06340.17050.0107-0.02340.13370.02610.149832.497538.200887.8547
31.0244-0.46120.04571.4989-0.4311.77790.06290.06420.1033-0.0989-0.0130.1549-0.0027-0.2582-0.04930.3185-0.0457-0.06950.1740.03660.251520.379359.533275.0342
41.4740.06750.32872.03140.14151.27160.044-0.3292-0.09980.1662-0.0211-0.04050.0299-0.1417-0.02490.15990.00310.02390.23280.05060.137919.840619.8485112.8218
51.82420.49211.28250.35280.52231.0661-0.0336-0.23560.06350.2321-0.20810.43840.2574-0.81540.03620.1561-0.11160.03250.5172-0.06250.3266-2.529310.071393.1171
61.28441.32471.51732.88232.07852.98880.1059-0.1861-0.06420.2407-0.1291-0.0270.2301-0.13580.01430.10780.00760.00810.15650.02650.119921.855815.1189103.1328
70.43790.36190.48770.5607-0.08153.77310.0473-0.0081-0.15330.0566-0.0319-0.11970.30050.0170.00150.16840.0596-0.00160.14790.02240.221328.25719.109493.6443
80.64820.028-0.31120.87180.35080.3044-0.00510.09010.0462-0.1119-0.05920.1931-0.0864-0.28670.03350.12110.0481-0.02470.2126-0.00530.184112.901128.731590.7186
90.75470.06380.06570.79840.25191.07940.0248-0.02330.02610.0264-0.0930.2714-0.0944-0.34360.04460.10840.0515-0.0050.2528-0.02460.20438.004126.691895.5882
100.84460.11420.09591.320.09661.72440.09240.0929-0.1838-0.2385-0.16010.22670.4221-0.43030.0490.2495-0.0531-0.05560.2614-0.060.27226.56231.631572.9126
111.3427-0.18990.33321.9209-0.01462.46080.11030.1116-0.1203-0.2077-0.13330.13490.3342-0.29720.0160.2135-0.0217-0.04350.1706-0.03940.19211.62084.296873.6307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 87 )A26 - 87
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 369 )A88 - 369
3X-RAY DIFFRACTION3chain 'A' and (resid 370 through 568 )A370 - 568
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 87 )B28 - 87
5X-RAY DIFFRACTION5chain 'B' and (resid 88 through 127 )B88 - 127
6X-RAY DIFFRACTION6chain 'B' and (resid 128 through 154 )B128 - 154
7X-RAY DIFFRACTION7chain 'B' and (resid 155 through 194 )B155 - 194
8X-RAY DIFFRACTION8chain 'B' and (resid 195 through 247 )B195 - 247
9X-RAY DIFFRACTION9chain 'B' and (resid 248 through 369 )B248 - 369
10X-RAY DIFFRACTION10chain 'B' and (resid 370 through 433 )B370 - 433
11X-RAY DIFFRACTION11chain 'B' and (resid 434 through 568 )B434 - 568

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