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- PDB-6upm: Crystal structure of T467A variant of cytosolic fumarate hydratas... -

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Basic information

Entry
Database: PDB / ID: 6upm
TitleCrystal structure of T467A variant of cytosolic fumarate hydratase from Leishmania major in a complex with S-malate
ComponentsFumarate hydratase 2Fumarase
KeywordsLYASE / fumarate hydratase / fumarase / Leishmania major / substrate / S-malate / variant T467A
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-hydroxybutanedioic acid / IRON/SULFUR CLUSTER / Fumarate hydratase 2
Similarity search - Component
Biological speciesLeishmania major strain Friedlin (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 17, 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
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

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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)134,1238
Polymers132,9672
Non-polymers1,1566
Water15,619867
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-81 kcal/mol
Surface area33970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.616, 84.718, 239.669
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:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 28 through 54 or (resid 55...A28 - 54
121(chain A and (resid 28 through 54 or (resid 55...A55
131(chain A and (resid 28 through 54 or (resid 55...A28 - 568
141(chain A and (resid 28 through 54 or (resid 55...A28 - 568
151(chain A and (resid 28 through 54 or (resid 55...A28 - 568
161(chain A and (resid 28 through 54 or (resid 55...A28 - 568
171(chain A and (resid 28 through 54 or (resid 55...A28 - 568
181(chain A and (resid 28 through 54 or (resid 55...A28 - 568
211(chain B and (resid 28 through 43 or (resid 44...B28 - 43
221(chain B and (resid 28 through 43 or (resid 44...B44
231(chain B and (resid 28 through 43 or (resid 44...B28 - 568
241(chain B and (resid 28 through 43 or (resid 44...B28 - 568
251(chain B and (resid 28 through 43 or (resid 44...B28 - 568
261(chain B and (resid 28 through 43 or (resid 44...B28 - 568
271(chain B and (resid 28 through 43 or (resid 44...B28 - 568
281(chain B and (resid 28 through 43 or (resid 44...B0
291(chain B and (resid 28 through 43 or (resid 44...B28 - 568
2101(chain B and (resid 28 through 43 or (resid 44...B28 - 568
2111(chain B and (resid 28 through 43 or (resid 44...B28 - 568

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Components

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


Mass: 66483.445 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
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / 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 / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 867 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.87 %
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, 12 mM S-Malate

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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: cryo-cooled 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: 2.03→50 Å / Num. obs: 87005 / % possible obs: 99.6 % / Redundancy: 5.5 % / CC1/2: 0.445 / Net I/σ(I): 7.7
Reflection shellResolution: 2.03→2.07 Å / Num. unique obs: 87005 / CC1/2: 0.445

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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: 2.03→48.919 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.76
RfactorNum. reflection% reflection
Rfree0.193 4346 5 %
Rwork0.1563 --
obs0.1581 86905 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.44 Å2 / Biso mean: 25.2945 Å2 / Biso min: 9.19 Å2
Refinement stepCycle: final / Resolution: 2.03→48.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8188 0 46 867 9101
Biso mean--25.25 34.47 -
Num. residues----1063
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2998X-RAY DIFFRACTION3.446TORSIONAL
12B2998X-RAY DIFFRACTION3.446TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.03-2.05310.31181400.2592265897
2.0531-2.07720.24861380.2514260898
2.0772-2.10260.24581450.2328276099
2.1026-2.12920.26651410.2224268899
2.1292-2.15720.27281410.2137268099
2.1572-2.18670.23721470.2088278499
2.1867-2.2180.27551390.20042651100
2.218-2.25110.26021440.20812732100
2.2511-2.28630.25061420.19832709100
2.2863-2.32380.21271460.19042749100
2.3238-2.36380.2391450.17912758100
2.3638-2.40680.2171430.17242718100
2.4068-2.45310.2141430.17142730100
2.4531-2.50320.22781460.1662754100
2.5032-2.55760.2041440.15872738100
2.5576-2.61710.2091430.16082735100
2.6171-2.68250.19391450.15172737100
2.6825-2.7550.18681450.1477277499
2.755-2.83610.19661440.14582722100
2.8361-2.92760.20211440.14142740100
2.9276-3.03230.1791470.13312787100
3.0323-3.15360.15841460.13762775100
3.1536-3.29710.19461460.14022768100
3.2971-3.47090.18821450.13172749100
3.4709-3.68830.16581470.12712807100
3.6883-3.9730.15661460.12552785100
3.973-4.37260.16081490.12312811100
4.3726-5.00480.11991480.11812826100
5.0048-6.30340.19461500.1572842100
6.3034-48.9190.17191570.1678298499
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)
10.4091-0.06680.11120.7071-0.31240.8698-0.0322-0.0740.03510.1066-0.0472-0.0925-0.17780.08020.08470.1835-0.0169-0.04330.16780.01640.177135.208942.645897.5459
20.7259-0.1066-0.0021.31920.46481.1181-0.05750.03470.0156-0.0857-0.02380.0623-0.11670.00060.07190.0848-0.00340.00540.10750.03420.111826.454233.842587.235
30.40960.0688-0.02791.0579-0.37840.6059-0.05830.04070.0969-0.05740.0450.0714-0.1508-0.00070.03410.174-0.0147-0.03370.14430.01690.147127.264845.874280.0375
42.17170.13160.34362.44730.51052.22910.12190.0290.04650.0253-0.04560.10270.0033-0.124-0.0640.2813-0.0303-0.03070.12070.06010.18621.830358.268574.4444
51.34730.08520.32512.01630.03241.20180.0385-0.2791-0.10860.1938-0.0077-0.0640.0388-0.1144-0.02580.1754-0.00040.01760.22040.04420.111719.566920.5287112.9913
62.36270.10081.25820.91150.60521.0056-0.0465-0.2063-0.12390.1393-0.03690.35540.1572-0.5493-0.04170.153-0.07740.03650.34870.00750.2478-2.406910.06792.8707
71.26191.17641.2162.87181.77922.23210.1429-0.1468-0.13970.1929-0.0562-0.1050.1482-0.1154-0.07520.1174-0.0041-0.00150.15510.04420.117721.794715.1209102.899
80.4720.3540.18810.9667-0.17472.89130.0708-0.0242-0.16460.0781-0.0072-0.09560.2280.0977-0.04710.17640.0541-0.01670.17120.02340.221728.01228.810592.886
90.40390.1559-0.36881.14680.32020.8661-0.01020.0330.0593-0.08360.00390.1183-0.0381-0.1188-0.01560.07440.0111-0.00370.1309-0.00820.126813.532328.698391.2342
100.78790.38490.03011.09820.19820.6342-0.02050.02310.09390.0102-0.00840.2365-0.0824-0.21350.03330.1050.0504-0.00970.1915-0.00460.17066.701730.330192.1321
110.4235-0.03620.27180.56810.17921.54580.0659-0.0029-0.1155-0.0802-0.06370.08660.2935-0.20750.00830.1821-0.0287-0.01910.14210.00030.191610.07784.97877.1947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 184 )A28 - 184
2X-RAY DIFFRACTION2chain 'A' and (resid 185 through 247 )A185 - 247
3X-RAY DIFFRACTION3chain 'A' and (resid 248 through 495 )A248 - 495
4X-RAY DIFFRACTION4chain 'A' and (resid 496 through 568 )A496 - 568
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 87 )B28 - 87
6X-RAY DIFFRACTION6chain 'B' and (resid 88 through 127 )B88 - 127
7X-RAY DIFFRACTION7chain 'B' and (resid 128 through 154 )B128 - 154
8X-RAY DIFFRACTION8chain 'B' and (resid 155 through 194 )B155 - 194
9X-RAY DIFFRACTION9chain 'B' and (resid 195 through 247 )B195 - 247
10X-RAY DIFFRACTION10chain 'B' and (resid 248 through 345 )B248 - 345
11X-RAY DIFFRACTION11chain 'B' and (resid 346 through 568 )B346 - 568

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