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- PDB-6uqb: Crystal structure of R471A variant of cytosolic fumarate hydratas... -

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Basic information

Entry
Database: PDB / ID: 6uqb
TitleCrystal structure of R471A variant of cytosolic fumarate hydratase from Leishmania major in a complex with S-malate and malonate
ComponentsFumarate hydratase 2
KeywordsLYASE / fumarate hydratase / fumarase / Leishmania major / variant H334A / substrate / S-malate / inhibitor / malonate
Function / homology
Function and homology information


fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / glycosome / ciliary plasm / tricarboxylic acid cycle / 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 / tricarboxylic acid cycle / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding / cytoplasm / cytosol
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-hydroxybutanedioic acid / MALONIC ACID / IRON/SULFUR CLUSTER / Fumarate hydratase 2
Similarity search - Component
Biological speciesLeishmania major strain Friedlin (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 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 18, 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 ...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 / struct_ncs_dom_lim
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_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_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.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 / _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)134,42712
Polymers132,8552
Non-polymers1,57210
Water16,520917
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10650 Å2
ΔGint-105 kcal/mol
Surface area34130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.462, 84.943, 240.266
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
13ASPASPALAALA(chain A and (resid 28 through 54 or (resid 55...AA28 - 56864 - 604
14ASPASPALAALA(chain A and (resid 28 through 54 or (resid 55...AA28 - 56864 - 604
15ASPASPALAALA(chain A and (resid 28 through 54 or (resid 55...AA28 - 56864 - 604
16ASPASPALAALA(chain A and (resid 28 through 54 or (resid 55...AA28 - 56864 - 604
17ASPASPALAALA(chain A and (resid 28 through 54 or (resid 55...AA28 - 56864 - 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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fumarate hydratase 2 / LmFH-2


Mass: 66427.352 Da / Num. of mol.: 2 / Mutation: R471A
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, 927 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 917 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
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, 12 mM RS-malate, 4.8 mM succinate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 98175 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC1/2: 0.815 / Net I/σ(I): 16
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 98175 / CC1/2: 0.815

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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: 1.951→49.043 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.96
RfactorNum. reflection% reflection
Rfree0.1742 4905 5 %
Rwork0.1434 --
obs0.145 98073 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.42 Å2 / Biso mean: 28.859 Å2 / Biso min: 10.98 Å2
Refinement stepCycle: final / Resolution: 1.951→49.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8185 0 74 919 9178
Biso mean--27.29 38.2 -
Num. residues----1067
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3046X-RAY DIFFRACTION4.549TORSIONAL
12B3046X-RAY DIFFRACTION4.549TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9514-1.97360.22721520.2006289794
1.9736-1.99680.23061620.18773059100
1.9968-2.02120.23211620.18253083100
2.0212-2.04680.20821610.17783062100
2.0468-2.07370.2331620.173068100
2.0737-2.10210.20291620.15613076100
2.1021-2.13210.16231600.15723052100
2.1321-2.1640.2041610.15493061100
2.164-2.19780.20291640.14983116100
2.1978-2.23380.19211630.14523097100
2.2338-2.27230.19431600.15043042100
2.2723-2.31370.19321630.15193095100
2.3137-2.35820.19151640.14733104100
2.3582-2.40630.20711620.15193076100
2.4063-2.45860.1891620.14663081100
2.4586-2.51580.16791630.14283102100
2.5158-2.57870.19411630.13913089100
2.5787-2.64840.16911620.14223098100
2.6484-2.72640.16571640.13523118100
2.7264-2.81430.17031630.14153087100
2.8143-2.91490.20771630.14223098100
2.9149-3.03160.1641650.14123120100
3.0316-3.16960.16991630.14573118100
3.1696-3.33660.19261660.1433138100
3.3366-3.54560.16521650.13393146100
3.5456-3.81930.14871670.12713160100
3.8193-4.20350.14141650.12373143100
4.2035-4.81120.11641680.11233190100
4.8112-6.05990.17941700.14643232100
6.0599-49.0430.17851780.16543360100
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)
10.36150.0333-0.00510.79-0.14651.008-0.0143-0.05750.0340.0844-0.0628-0.0775-0.20750.1220.08220.2114-0.0035-0.04950.18260.01330.196634.24280.6597-22.1474
20.56340.13640.12660.82080.1031.0284-0.05830.02360.0131-0.09620.0088-0.0892-0.15310.1230.04750.1430.0074-0.00580.13390.02180.143233.2813-9.8511-35.302
31.3118-0.3790.37762.0059-0.32662.24370.09940.02260.048-0.0633-0.06640.26060.0204-0.3088-0.02890.3299-0.0275-0.06070.18440.0250.262819.563817.3199-45.3666
41.44510.19660.3421.97260.19841.19060.0481-0.3071-0.10030.2565-0.0699-0.01560.1054-0.11670.01890.21890.00130.03720.23640.03440.141319.4975-21.9098-6.9592
52.26880.23971.26750.54450.59571.1274-0.0804-0.16430.01960.1093-0.10960.44440.1699-0.6754-0.10570.1862-0.09590.04650.4458-0.07330.342-2.6928-31.8193-27.1215
61.291.3591.28482.90311.82182.58210.0773-0.1652-0.10330.2104-0.1189-0.06150.2018-0.15160.03620.14310.01050.01430.16260.03430.125521.7799-27.3477-17.0487
70.54340.53560.20390.70170.55442.79140.0451-0.0227-0.14850.1119-0.0347-0.08790.33740.0081-0.00340.19560.05630.00090.16490.03640.221328.0979-33.3622-26.828
80.7611-0.00730.04330.96950.06610.8215-0.03310.01820.0593-0.0019-0.04820.2057-0.0951-0.2190.06670.11690.0469-0.010.1937-0.01830.184311.6862-12.4907-26.7707
90.87230.08990.12660.66360.36650.5985-0.0066-0.03740.00340.0202-0.08870.2949-0.0065-0.3030.04420.11210.02130.00340.2594-0.0480.22326.291-18.6048-24.6256
100.8215-0.04610.18171.35980.22371.77640.06280.0562-0.0865-0.1677-0.14130.18060.2918-0.30450.060.223-0.0295-0.0340.1872-0.05060.20539.8527-38.749-47.1317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 194 )A28 - 194
2X-RAY DIFFRACTION2chain 'A' and (resid 195 through 373 )A195 - 373
3X-RAY DIFFRACTION3chain 'A' and (resid 374 through 568 )A374 - 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 297 )B195 - 297
9X-RAY DIFFRACTION9chain 'B' and (resid 298 through 369 )B298 - 369
10X-RAY DIFFRACTION10chain 'B' and (resid 370 through 568 )B370 - 568

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