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- PDB-4bgi: Crystal structure of InhA(S94A) mutant in complex with OH-141 -

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Basic information

Entry
Database: PDB / ID: 4bgi
TitleCrystal structure of InhA(S94A) mutant in complex with OH-141
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / TUBERCULOSIS DRUG
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / response to antibiotic / plasma membrane
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-I4I / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsPojer, F. / Hartkoorn, R.C. / Cole, S.T.
CitationJournal: Nat. Chem. Biol. / Year: 2014
Title: Pyridomycin bridges the NADH- and substrate-binding pockets of the enoyl reductase InhA.
Authors: Hartkoorn, R.C. / Pojer, F. / Read, J.A. / Gingell, H. / Neres, J. / Horlacher, O.P. / Altmann, K.H. / Cole, S.T.
History
DepositionMar 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 2.0Nov 21, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,67412
Polymers180,0986
Non-polymers3,5766
Water8,467470
1
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5848
Polymers120,0654
Non-polymers2,5194
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_545x+1/2,y-1/2,z1
identity operation1_555x,y,z1
Buried area17390 Å2
ΔGint-119.3 kcal/mol
Surface area34580 Å2
MethodPISA
2
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,1798
Polymers120,0654
Non-polymers2,1144
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14260 Å2
ΔGint-99.9 kcal/mol
Surface area35550 Å2
MethodPISA
3
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5848
Polymers120,0654
Non-polymers2,5194
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_545x+1/2,y-1/2,z1
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.442, 82.450, 189.645
Angle α, β, γ (deg.)90.00, 95.63, 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: 30016.314 Da / Num. of mol.: 6 / Mutation: S94A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-I4I / 3-hydroxy-N-[(2R,5R,6S,9S,10S,11R)-10-hydroxy-5,11-dimethyl-3,7,12-trioxo-2-(propan-2-yl)-9-(pyridin-3-ylmethyl)-1,4-dioxa-8-azacyclododecan-6-yl]pyridine-2-carboxamide


Mass: 528.554 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H32N4O8
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.17 Å3/Da / Density % sol: 43.31 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 171328 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 30.46 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 8.3
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 2.3 / % possible all: 91.3

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DTI

4dti


Resolution: 2.09→30.6 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.8759 / SU R Cruickshank DPI: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.237 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.185
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 4530 5.01 %RANDOM
Rwork0.2107 ---
obs0.2121 90347 98.99 %-
Displacement parametersBiso mean: 37.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.0592 Å20 Å2-0.0664 Å2
2---0.3233 Å20 Å2
3---0.3825 Å2
Refine analyzeLuzzati coordinate error obs: 0.276 Å
Refinement stepCycle: LAST / Resolution: 2.09→30.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11651 0 246 470 12367
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112146HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1116527HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4141SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes267HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1904HARMONIC5
X-RAY DIFFRACTIONt_it12146HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion20.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1630SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14256SEMIHARMONIC4
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 273 4.7 %
Rwork0.2424 5538 -
all0.244 5811 -
obs--98.99 %

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