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- PDB-5vrm: CRYSTAL STRUCTURE OF THE INHA FROM MYCOBACTERIUM TUBERCULOSIS IN ... -

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Basic information

Entry
Database: PDB / ID: 5vrm
TitleCRYSTAL STRUCTURE OF THE INHA FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH AN12855, EBSI 4333.
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / INHA / ENOYL-ACYL REDUCTASE / TUBERCULOSIS
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / response to antibiotic
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9JJ / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAbendroth, J. / Edwards, T.E. / Lorimer, D.
CitationJournal: Life Sci Alliance / Year: 2018
Title: Discovery of a cofactor-independent inhibitor ofMycobacterium tuberculosisInhA.
Authors: Xia, Y. / Zhou, Y. / Carter, D.S. / McNeil, M.B. / Choi, W. / Halladay, J. / Berry, P.W. / Mao, W. / Hernandez, V. / O'Malley, T. / Korkegian, A. / Sunde, B. / Flint, L. / Woolhiser, L.K. / ...Authors: Xia, Y. / Zhou, Y. / Carter, D.S. / McNeil, M.B. / Choi, W. / Halladay, J. / Berry, P.W. / Mao, W. / Hernandez, V. / O'Malley, T. / Korkegian, A. / Sunde, B. / Flint, L. / Woolhiser, L.K. / Scherman, M.S. / Gruppo, V. / Hastings, C. / Robertson, G.T. / Ioerger, T.R. / Sacchettini, J. / Tonge, P.J. / Lenaerts, A.J. / Parish, T. / Alley, M.
History
DepositionMay 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,1788
Polymers115,3484
Non-polymers3,8304
Water1,09961
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7952
Polymers28,8371
Non-polymers9571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7952
Polymers28,8371
Non-polymers9571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7952
Polymers28,8371
Non-polymers9571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7952
Polymers28,8371
Non-polymers9571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14100 Å2
ΔGint-97 kcal/mol
Surface area31290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.350, 92.680, 101.930
Angle α, β, γ (deg.)90.00, 105.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-ACP reductase / FAS-II enoyl-ACP reductase / NADH-dependent 2-trans-enoyl-ACP reductase


Mass: 28837.057 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: inhA, MT1531 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P9WGR0, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-9JJ / [[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3-oxidanyl-4-[[1-oxidanyl-6-[4-(trifluoromethyl)phenoxy]-3~{H}-2,1$l^{4}-benzoxaborol-1-yl]oxy]oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 957.459 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C35H37BF3N7O17P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: INHA, ENOYL-ACP REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS, R5645 AT 10.0 MG/ML (340UM), BATCH NUMBER 1526003A, IN 20MM PIPES PH 7.3, 50 MM NACL, WITH 3.5MM NAD+ (EBSI1606) AND 420UM AN2918 ...Details: INHA, ENOYL-ACP REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS, R5645 AT 10.0 MG/ML (340UM), BATCH NUMBER 1526003A, IN 20MM PIPES PH 7.3, 50 MM NACL, WITH 3.5MM NAD+ (EBSI1606) AND 420UM AN2918 (EBSI4012) AGAINST OPTIMIZATION SCREEN ACR_PEGISH_AMAC_DMSO_ADA WELL E4: 0.1M ADA/NAOH PH6.8, 12.0% W/V PEG 4,000, 0.25M AMMONIUM ACETATE, AND CRYO-PROTECTED IN 40% MPD WITH 0.1MM OF EACH COMPOUND; CRYSTAL TRACKING ID 249555E4 (BUV9-3), PH 6.80, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
PH range: 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→49.09 Å / Num. obs: 38978 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 56.44 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 22.82
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 17.742 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.526 / ESU R Free: 0.255
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1954 5 %RANDOM
Rwork0.192 ---
obs0.193 38978 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å2-0 Å2-1.2 Å2
2--3.16 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 239 61 7620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197731
X-RAY DIFFRACTIONr_bond_other_d0.0050.027180
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9610586
X-RAY DIFFRACTIONr_angle_other_deg0.9372.98216406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9151008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56323.563261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.695151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8831540
X-RAY DIFFRACTIONr_chiral_restr0.130.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218774
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021682
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7293.424059
X-RAY DIFFRACTIONr_mcbond_other1.7293.4194058
X-RAY DIFFRACTIONr_mcangle_it2.7265.1225058
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 141 -
Rwork0.263 2723 -
obs--99.93 %
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)
10.6950.01340.2691.37540.46641.3843-0.05350.0086-0.18470.0340.09090.05330.30490.2499-0.03740.16210.13440.02190.1246-0.00270.1113254.843416.3574118.9615
20.8858-0.4049-0.30611.3620.19441.72460.0330.01-0.1856-0.0019-0.18190.4794-0.2115-0.36510.14890.09230.1128-0.00210.1799-0.07190.2454228.743536.3883120.9843
31.1182-0.51560.07541.3544-0.33751.20.07680.02090.0759-0.0569-0.10840.006-0.6370.16950.03150.452-0.0388-0.01270.0539-0.0050.0302248.424659.8034114.8351
41.0906-0.29650.43681.2389-0.50051.1848-0.0731-0.03070.08510.2022-0.0383-0.256-0.32280.58040.11140.1465-0.0958-0.04950.4544-0.00950.0799271.838140.6488128.1546
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 300
2X-RAY DIFFRACTION2B2 - 300
3X-RAY DIFFRACTION3C3 - 300
4X-RAY DIFFRACTION4D3 - 300

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