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- PDB-6s7u: Fumarate hydratase of Mycobacterium tuberculosis in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6s7u
TitleFumarate hydratase of Mycobacterium tuberculosis in complex with formate and allosteric modulator N-(5-(Azepan-1-ylsulfonyl)-2-methoxyphenyl)-2-(1H-indol-3-yl)acetamide
ComponentsFumarate hydratase class II
KeywordsLYASE / Fumarate hydratase / Fumarase
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 / cytosol / cytoplasm
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarate lyase, conserved site ...Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / Chem-KZK / Fumarate hydratase class II / Fumarate hydratase class II
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å
AuthorsWhitehouse, A.J. / Libardo, M.D. / Kasbekar, M. / Brear, P. / Fischer, G. / Thomas, C.J. / Barry, C.E. / Boshoff, H.I. / Coyne, A.G. / Abell, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: J.Med.Chem. / Year: 2019
Title: Targeting of Fumarate Hydratase fromMycobacterium tuberculosisUsing Allosteric Inhibitors with a Dimeric-Binding Mode.
Authors: Whitehouse, A.J. / Libardo, M.D.J. / Kasbekar, M. / Brear, P.D. / Fischer, G. / Thomas, C.J. / Barry 3rd, C.E. / Boshoff, H.I.M. / Coyne, A.G. / Abell, C.
History
DepositionJul 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 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.name
Revision 1.2Jan 24, 2024Group: 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_conn.ptnr2_symmetry

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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)201,7459
Polymers200,7674
Non-polymers9785
Water30,5531696
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27630 Å2
ΔGint-154 kcal/mol
Surface area56460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.258, 96.662, 124.259
Angle α, β, γ (deg.)90.000, 102.750, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-642-

HOH

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Components

#1: Protein
Fumarate hydratase class II / Fumarase C / Aerobic fumarase / Iron-independent fumarase


Mass: 50191.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: fum, fumC, DSI35_09545, ERS007663_02818, ERS007679_02635, ERS007688_02307, ERS007722_03256, ERS023446_00966, ERS024276_01230, ERS027646_00759, ERS027653_00188, ERS027654_00515, ERS027659_00384, ...Gene: fum, fumC, DSI35_09545, ERS007663_02818, ERS007679_02635, ERS007688_02307, ERS007722_03256, ERS023446_00966, ERS024276_01230, ERS027646_00759, ERS027653_00188, ERS027654_00515, ERS027659_00384, ERS027661_00671, ERS027666_02275, ERS124361_03161, SAMEA2682864_03539, SAMEA2683035_02636
Plasmid: pNAN / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A045IXZ8, UniProt: P9WN93*PLUS, fumarate hydratase
#2: Chemical ChemComp-KZK / ~{N}-[5-(azepan-1-ylsulfonyl)-2-methoxy-phenyl]-2-(1~{H}-indol-3-yl)ethanamide


Mass: 441.543 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1696 / 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: 2.68 Å3/Da / Density % sol: 54.14 % / Mosaicity: 0.07 °
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: NaCl, Tris, TCEP, PEG3350, DMSO, magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.48→121.2 Å / Num. obs: 324139 / % possible obs: 96.2 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.055 / Rrim(I) all: 0.151 / Net I/σ(I): 8.4 / Num. measured all: 2395184 / Scaling rejects: 77
Reflection shell

Diffraction-ID: 1 / % possible all: 99.8

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.48-1.567.51.856366843490290.4420.7191.9931.1
4.67-121.27.10.05477139109070.9980.0210.05828.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
XDSdata reduction
Aimless0.7.2data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S43

6s43


Resolution: 1.48→121.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.068
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 16182 5 %RANDOM
Rwork0.1738 ---
obs0.175 307957 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 140.43 Å2 / Biso mean: 24.349 Å2 / Biso min: 5.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å2-0.31 Å2
2--0.14 Å20 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 1.48→121.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13431 0 67 1696 15194
Biso mean--28.42 33.11 -
Num. residues----1805
LS refinement shellResolution: 1.48→1.516 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.287 1189 -
Rwork0.287 23635 -
obs--99.78 %

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