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

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Basic information

Entry
Database: PDB / ID: 6unz
TitleCrystal structure of cytosolic fumarate hydratase from Leishmania major
Componentsfumarate hydratase 2
KeywordsLYASE / fumarate hydratase / fumarase / Leishmania major / holo
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 / 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
IRON/SULFUR CLUSTER / Fumarate hydratase 2
Similarity search - Component
Biological speciesLeishmania major strain Friedlin (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.195 Å
AuthorsFeliciano, P.R. / Drennan, C.L.
Funding support United States, Brazil, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
Sao Paulo Research Foundation (FAPESP)2014/22246-4 Brazil
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 14, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fumarate hydratase 2
B: fumarate hydratase 2
C: fumarate hydratase 2
D: fumarate hydratase 2
E: fumarate hydratase 2
F: fumarate hydratase 2
G: fumarate hydratase 2
H: fumarate hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)535,10518
Polymers532,1088
Non-polymers2,99710
Water543
1
A: fumarate hydratase 2
B: fumarate hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,8225
Polymers133,0272
Non-polymers7953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-84 kcal/mol
Surface area38010 Å2
MethodPISA
2
C: fumarate hydratase 2
D: fumarate hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,7304
Polymers133,0272
Non-polymers7032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-78 kcal/mol
Surface area38240 Å2
MethodPISA
3
E: fumarate hydratase 2
F: fumarate hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,8225
Polymers133,0272
Non-polymers7953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-88 kcal/mol
Surface area36210 Å2
MethodPISA
4
G: fumarate hydratase 2
H: fumarate hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,7304
Polymers133,0272
Non-polymers7032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-86 kcal/mol
Surface area37050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.094, 66.072, 238.085
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 29 or (resid 30 and (name...
21(chain B and (resid 29 or (resid 30 and (name...
31(chain C and (resid 29 through 31 or (resid 32...
41(chain D and (resid 29 through 31 or (resid 32...
51(chain E and (resid 29 or (resid 30 and (name...
61(chain F and (resid 29 or (resid 30 and (name...
71(chain G and (resid 29 or (resid 30 and (name...
81(chain H and (resid 29 or (resid 30 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 29 or (resid 30 and (name...A0
211(chain B and (resid 29 or (resid 30 and (name...B0
311(chain C and (resid 29 through 31 or (resid 32...C0
411(chain D and (resid 29 through 31 or (resid 32...D0
511(chain E and (resid 29 or (resid 30 and (name...E0
611(chain F and (resid 29 or (resid 30 and (name...F0
711(chain G and (resid 29 or (resid 30 and (name...G0
811(chain H and (resid 29 or (resid 30 and (name...H0

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Components

#1: Protein
fumarate hydratase 2


Mass: 66513.469 Da / Num. of mol.: 8
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


Mass: 351.640 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
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

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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
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 3.195→50 Å / Num. obs: 75134 / % possible obs: 90.4 % / Redundancy: 3 % / CC1/2: 0.334 / Net I/σ(I): 5
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 75134 / CC1/2: 0.334

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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: 3.195→49.708 Å / Cross valid method: THROUGHOUT / σ(F): 688.99 / Phase error: 29.79
RfactorNum. reflection% reflection
Rfree0.2888 3885 5.17 %
Rwork0.2453 --
obs0.2585 75107 90.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.75 Å2 / Biso mean: 63.242 Å2 / Biso min: 15.07 Å2
Refinement stepCycle: final / Resolution: 3.195→49.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31159 0 76 3 31238
Biso mean--68.52 41.73 -
Num. residues----4260
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A16151X-RAY DIFFRACTION8.112TORSIONAL
12B16151X-RAY DIFFRACTION8.112TORSIONAL
13C16151X-RAY DIFFRACTION8.112TORSIONAL
14D16151X-RAY DIFFRACTION8.112TORSIONAL
15E16151X-RAY DIFFRACTION8.112TORSIONAL
16F16151X-RAY DIFFRACTION8.112TORSIONAL
17G16151X-RAY DIFFRACTION8.112TORSIONAL
18H16151X-RAY DIFFRACTION8.112TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.197-3.25210.32861590.30473031319073
3.2521-3.31120.33891640.29493156332076
3.3112-3.37490.38511590.29313074323376
3.3749-3.44380.31781660.28593188335476
3.4438-3.51860.351720.29473221339379
3.5186-3.60040.32391790.28313355353482
3.6004-3.69050.29321810.28213494367584
3.6905-3.79020.34141830.28243479366285
3.7902-3.90170.31431840.27233512369685
3.9017-4.02750.34771780.26393537371586
4.0275-4.17140.31491900.26973575376587
4.1714-4.33830.28821950.26063667386288
4.3383-4.53560.27581880.24073534372285
4.5356-4.77450.30752000.23693856405692
4.7745-5.07330.26132090.24563939414895
5.0733-5.46450.3242080.25343892410094
5.4645-6.01340.34492100.2623961417194
6.0134-6.88110.29852010.24093765396690
6.8811-8.66050.23792150.21823997421294
8.6605-46.75260.25082110.22874086429793

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