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- PDB-5f91: Fumarate hydratase of Mycobacterium tuberculosis in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5f91
TitleFumarate hydratase of Mycobacterium tuberculosis in complex with formate and allosteric modulator (N-(5-(azepan-1-ylsulfonyl)-2-methoxyphenyl)-2-(4-oxo-3,4-dihydrophthalazin-1-yl)acetamide)
ComponentsFumarate hydratase class II
KeywordsLYASE/LYASE INHIBITOR / allostery / inhibitor / hydratase / metabolism / tuberculosis / modulation / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) ...Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5WJ / FORMIC ACID / Fumarate hydratase class II / Fumarate hydratase class II
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsKasbekar, M. / Fischer, G. / Mott, B.T. / Yasgar, A. / Hyvonen, M. / Boshoff, H.I. / Abell, C. / Barry, C.E. / Thomas, C.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Selective small molecule inhibitor of the Mycobacterium tuberculosis fumarate hydratase reveals an allosteric regulatory site.
Authors: Kasbekar, M. / Fischer, G. / Mott, B.T. / Yasgar, A. / Hyvonen, M. / Boshoff, H.I. / Abell, C. / Barry, C.E. / Thomas, C.J.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fumarate hydratase class II
B: Fumarate hydratase class II
C: Fumarate hydratase class II
D: Fumarate hydratase class II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,64212
Polymers210,4774
Non-polymers1,1648
Water27,9051549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27670 Å2
ΔGint-181 kcal/mol
Surface area54150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.212, 96.497, 124.376
Angle α, β, γ (deg.)90.00, 102.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-683-

HOH

21D-931-

HOH

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Components

#1: Protein
Fumarate hydratase class II / Fumarase C


Mass: 52619.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: fumC, fum, MT1130 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WN92, UniProt: P9WN93*PLUS, fumarate hydratase
#2: Chemical ChemComp-5WJ / ~{N}-[5-(azepan-1-ylsulfonyl)-2-methoxy-phenyl]-2-(4-oxidanylidene-3~{H}-phthalazin-1-yl)ethanamide


Mass: 470.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26N4O5S
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1549 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 17% PEG3350, 5% DMSO, 200 mM MgFormate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.998→48.806 Å / Num. obs: 130081 / % possible obs: 95.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.074 / Rsym value: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 1.998→2.004 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.1 / % possible all: 62.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
autoPROCdata scaling
XDSdata reduction
BUCCANEERmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NO9

3no9


Resolution: 1.998→48.806 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1939 6505 5 %Random
Rwork0.1508 ---
obs0.1529 130054 95.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→48.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13225 0 74 1549 14848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713520
X-RAY DIFFRACTIONf_angle_d0.98618385
X-RAY DIFFRACTIONf_dihedral_angle_d13.1424948
X-RAY DIFFRACTIONf_chiral_restr0.0392194
X-RAY DIFFRACTIONf_plane_restr0.0052474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.998-2.02060.30962090.24583747X-RAY DIFFRACTION88
2.0206-2.04440.25342130.21524225X-RAY DIFFRACTION97
2.0444-2.06930.27212350.22364147X-RAY DIFFRACTION97
2.0693-2.09550.26862080.21884183X-RAY DIFFRACTION97
2.0955-2.12310.27312270.21034215X-RAY DIFFRACTION97
2.1231-2.15220.2512110.19284138X-RAY DIFFRACTION96
2.1522-2.18290.26142240.18654125X-RAY DIFFRACTION96
2.1829-2.21550.21952210.17814199X-RAY DIFFRACTION97
2.2155-2.25010.20881890.17284219X-RAY DIFFRACTION97
2.2501-2.2870.20242370.16474145X-RAY DIFFRACTION97
2.287-2.32640.21132430.15564177X-RAY DIFFRACTION97
2.3264-2.36870.22222370.16544094X-RAY DIFFRACTION96
2.3687-2.41430.20232320.16134082X-RAY DIFFRACTION95
2.4143-2.46360.20232110.15764188X-RAY DIFFRACTION97
2.4636-2.51710.22252400.15774198X-RAY DIFFRACTION97
2.5171-2.57570.21971950.15354162X-RAY DIFFRACTION96
2.5757-2.64010.19582150.1514177X-RAY DIFFRACTION96
2.6401-2.71150.21542100.14864166X-RAY DIFFRACTION96
2.7115-2.79120.19742130.15214087X-RAY DIFFRACTION95
2.7912-2.88130.20142140.14784181X-RAY DIFFRACTION96
2.8813-2.98430.20272250.14934144X-RAY DIFFRACTION96
2.9843-3.10380.19661970.14644158X-RAY DIFFRACTION95
3.1038-3.2450.19632160.14584082X-RAY DIFFRACTION94
3.245-3.4160.172340.14254127X-RAY DIFFRACTION95
3.416-3.630.18382290.13394063X-RAY DIFFRACTION94
3.63-3.91020.18081900.13214078X-RAY DIFFRACTION93
3.9102-4.30340.15232100.11894087X-RAY DIFFRACTION93
4.3034-4.92570.13842120.11464009X-RAY DIFFRACTION92
4.9257-6.20380.16952080.13754028X-RAY DIFFRACTION92
6.2038-48.82060.13622000.13493918X-RAY DIFFRACTION88

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