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- PDB-1zid: LONG FATTY ACID CHAIN ENOYL-ACP REDUCTASE (INHA) IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 1zid
TitleLONG FATTY ACID CHAIN ENOYL-ACP REDUCTASE (INHA) IN COMPLEX WITH AN ISONICOTINIC-ACYL-NADH INHIBITOR
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
KeywordsOXIDOREDUCTASE / INHA ENZYME / ISONIAZID / MODIFIED NADH / ENOYL-ACP REDUCTASE / TUBERCULOSIS / MYCOLIC ACID BIOSYNTHESIS / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 activity (NAD(P)H) / 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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ZID / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / INITIAL PHASES DERIVED FROM NATIVE STRUCTURE (PDB ENTRY 1ENY) / Resolution: 2.7 Å
AuthorsRozwarski, D.A. / Jacobs Jr., W.R. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: Science / Year: 1998
Title: Modification of the NADH of the isoniazid target (InhA) from Mycobacterium tuberculosis.
Authors: Rozwarski, D.A. / Grant, G.A. / Barton, D.H. / Jacobs Jr., W.R. / Sacchettini, J.C.
#1: Journal: Science / Year: 1995
Title: Crystal Structure and Function of the Isoniazid Target of Mycobacterium Tuberculosis
Authors: Dessen, A. / Quemard, A. / Blanchard, J.S. / Jacobs Junior, W.R. / Sacchettini, J.C.
History
DepositionMar 25, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...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.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1622
Polymers28,3941
Non-polymers7691
Water1,22568
1
A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules

A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules

A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules

A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6488
Polymers113,5744
Non-polymers3,0744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_565x,x-y+1,-z+1/31
Buried area19810 Å2
ΔGint-130 kcal/mol
Surface area34370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.530, 100.530, 138.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE / INHA / ENOYL-ACP REDUCTASE


Mass: 28393.562 Da / Num. of mol.: 1 / Mutation: T2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-ZID / ISONICOTINIC-ACETYL-NICOTINAMIDE-ADENINE DINUCLEOTIDE


Mass: 768.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H30N8O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.58 Å3/Da / Density % sol: 65.6 %
Crystal growpH: 7.5
Details: 12% MPD, 4% DMSO, 50MM NACITRATE, 100 MM HEPES, PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 %methylpentanediol1reservoir
22 %dimethyl sulfoxide1reservoir
350 mMHEPES1reservoirpH7.5
425 mMsodium citrate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromator: 0.005 MM NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→10 Å / Num. obs: 10621 / % possible obs: 90.7 % / Observed criterion σ(I): 1 / Rsym value: 0.164 / Net I/σ(I): 11.3
Reflection shellResolution: 2.7→2.77 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.343 / % possible all: 49.5
Reflection
*PLUS
Rmerge(I) obs: 0.164
Reflection shell
*PLUS
% possible obs: 50 % / Rmerge(I) obs: 0.343

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: INITIAL PHASES DERIVED FROM NATIVE STRUCTURE (PDB ENTRY 1ENY)
Starting model: NATIVE STRUCTURE (PDB ENTRY 1ENY)

1eny


Resolution: 2.7→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1074 9.2 %RANDOM IN SHELLS
Rwork0.202 ---
obs0.202 10422 89 %-
Displacement parametersBiso mean: 24.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.3 Å
Luzzati d res low-4.5 Å
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 52 68 2114
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.433 44 4.6 %
Rwork0.278 394 -
obs--45 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.NADTOPOLOGY.NAD
X-RAY DIFFRACTION3PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.2

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