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- PDB-2aq8: Crystal structure of wild-type of Enoyl-ACP(CoA) reductase from M... -

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Basic information

Entry
Database: PDB / ID: 2aq8
TitleCrystal structure of wild-type of Enoyl-ACP(CoA) reductase from Mycobacterium tuberculosis in complex with NADH.
ComponentsEnoyl-Acyl-carrier-protein reductase
KeywordsOXIDOREDUCTASE / ENOYL-ACYL CARRIER PROTEIN
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
LYSINE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsOliveira, J.S. / Pereira, J.H. / Rodrigues, N.C. / Canduri, F. / Basso, L.A. / de Azevedo Jr., W.F. / Santos, D.S.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystallographic and Pre-steady-state Kinetics Studies on Binding of NADH to Wild-type and Isoniazid-resistant Enoyl-ACP(CoA) Reductase Enzymes from Mycobacterium tuberculosis.
Authors: Oliveira, J.S. / Pereira, J.H. / Canduri, F. / Rodrigues, N.C. / de Souza, O.N. / de Azevedo Jr., W.F. / Basso, L.A. / Santos, D.S.
History
DepositionAug 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2013Group: Non-polymer description
Revision 1.4Jul 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 23, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms / struct_conn

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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)29,3673
Polymers28,5551
Non-polymers8132
Water3,171176
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)117,47012
Polymers114,2194
Non-polymers3,2518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_545x,x-y-1,-z+1/31
Buried area18670 Å2
ΔGint-125 kcal/mol
Surface area32260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.022, 96.022, 138.164
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-444-

HOH

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Components

#1: Protein Enoyl-Acyl-carrier-protein reductase / NADH-dependent enoyl-ACP reductase


Mass: 28554.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA / Plasmid: pET-23d(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.05 M Sodium citrate, 0.05 M Hepes, 8-15% 2-Methyl-2-4-pentanediol (MPD), pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 9, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.431 Å / Relative weight: 1
ReflectionResolution: 1.92→39.84 Å / Num. obs: 26972 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.92→2.03 Å / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
SCALAdata scaling
AMoREphasing
X-PLORrefinement
CCP4(SCALA)data scaling
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ENY

1eny


Resolution: 1.92→33.24 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.807 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 1446 5.1 %RANDOM
Rwork0.18746 ---
obs0.18876 26972 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.316 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.92→33.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 49 176 2209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222074
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.751.9792823
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9845266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69723.92479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6515325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8251513
X-RAY DIFFRACTIONr_chiral_restr0.1390.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021551
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.21191
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21469
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2212
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.2106
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9541.51346
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36522100
X-RAY DIFFRACTIONr_scbond_it2.5343821
X-RAY DIFFRACTIONr_scangle_it3.8724.5723
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.921→1.971 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 95 -
Rwork0.306 1801 -
obs--90.07 %

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