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- PDB-1bvr: M.TB. ENOYL-ACP REDUCTASE (INHA) IN COMPLEX WITH NAD+ AND C16-FAT... -

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Basic information

Entry
Database: PDB / ID: 1bvr
TitleM.TB. ENOYL-ACP REDUCTASE (INHA) IN COMPLEX WITH NAD+ AND C16-FATTY-ACYL-SUBSTRATE
ComponentsPROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
KeywordsOXIDOREDUCTASE / NADH-DEPENDENT ENOYL-ACP REDUCTASE / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / 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 / fatty acid biosynthetic process ...enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / 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 / fatty acid biosynthetic process / response to antibiotic / plasma membrane
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-THT / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRozwarski, D.A. / Vilcheze, C. / Sugantino, M. / Bittman, R. / Jacobs, W. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Crystal structure of the Mycobacterium tuberculosis enoyl-ACP reductase, InhA, in complex with NAD+ and a C16 fatty acyl substrate.
Authors: Rozwarski, D.A. / Vilcheze, C. / Sugantino, M. / Bittman, R. / Sacchettini, J.C.
History
DepositionSep 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Mar 10, 2021Group: Derived calculations / Category: struct_conn / struct_site
Item: _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
B: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
C: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
D: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
E: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
F: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,95216
Polymers170,5426
Non-polymers5,41110
Water11,944663
1
C: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
D: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
E: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
F: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,06310
Polymers113,6944
Non-polymers3,3696
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20640 Å2
ΔGint-126 kcal/mol
Surface area34160 Å2
MethodPISA
2
A: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
B: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8896
Polymers56,8472
Non-polymers2,0424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-42 kcal/mol
Surface area20630 Å2
MethodPISA
3
A: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
B: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
hetero molecules

A: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
B: PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,77812
Polymers113,6944
Non-polymers4,0848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area22570 Å2
ΔGint-132 kcal/mol
Surface area33240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.080, 83.450, 192.810
Angle α, β, γ (deg.)90.00, 95.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1409-

HOH

21B-1418-

HOH

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Components

#1: Protein
PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE) / INHA


Mass: 28423.586 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-THT / TRANS-2-HEXADECENOYL-(N-ACETYL-CYSTEAMINE)-THIOESTER / C16-FATTY-ACYL-SUBSTRATE-MIMIC


Mass: 357.594 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H39NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 53 %
Crystal growpH: 6.8
Details: 10% PEG-4000, 6% DMSO, 100 MM AMMONIUM ACETATE, AND 100 MM ADA, PH 6.8
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %PEG40001reservoir
26 %1reservoirMe2SO
3100 mMammonium acetate1reservoir
4100 mMADA1reservoir
510 mg/mlprotain1drop

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→10 Å / Num. obs: 30077 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rsym value: 0.162 / Net I/σ(I): 7.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 0.5 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.255 / % possible all: 58
Reflection
*PLUS
Num. obs: 35800 / Rmerge(I) obs: 0.162
Reflection shell
*PLUS
% possible obs: 79.3 % / Redundancy: 1 % / Num. unique obs: 3029 / Rmerge(I) obs: 0.255

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ENY

1eny


Resolution: 2.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.344 -10 %RANDOM
Rwork0.217 ---
obs0.217 34838 90.2 %-
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11964 0 360 663 12987
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.396 -10 %
Rwork0.298 2584 -
obs--67.6 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 10 Å / σ(F): 3 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / Rfactor Rfree: 0.396 / % reflection Rfree: 10 % / Rfactor Rwork: 0.298 / Rfactor obs: 0.298

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