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Basic information

Entry
Database: PDB / ID: 7lg9
TitleChsB1
Components3-ketoacyl-ACP reductase
KeywordsOXIDOREDUCTASE / short-chain type alcohol dehydrogenase/reductase hydroxyacyl-CoA dehydrogenase
Function / homology3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / 3-ketoacyl-ACP reductase
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsYuan, T. / Werman, J.M. / Yin, X. / Yang, M. / Garcia-Diaz, M. / Sampson, N.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1AI134054 United States
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Enzymatic beta-Oxidation of the Cholesterol Side Chain in Mycobacterium tuberculosis Bifurcates Stereospecifically at Hydration of 3-Oxo-cholest-4,22-dien-24-oyl-CoA.
Authors: Yuan, T. / Werman, J.M. / Yin, X. / Yang, M. / Garcia-Diaz, M. / Sampson, N.S.
History
DepositionJan 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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: 3-ketoacyl-ACP reductase
B: 3-ketoacyl-ACP reductase


Theoretical massNumber of molelcules
Total (without water)65,5292
Polymers65,5292
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-51 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.854, 80.131, 163.532
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 3-ketoacyl-ACP reductase / 3-oxoacyl-ACP reductase


Mass: 32764.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: fabG_8, fabG_1, fabG_2, fabG_4, fabG_6, fabG_7, DSI38_08445, E5M52_16205, ERS007665_00489, ERS007670_00458, ERS007679_00994, ERS007681_00640, ERS007741_01258, ERS013471_03025, ERS023446_03243, ...Gene: fabG_8, fabG_1, fabG_2, fabG_4, fabG_6, fabG_7, DSI38_08445, E5M52_16205, ERS007665_00489, ERS007670_00458, ERS007679_00994, ERS007681_00640, ERS007741_01258, ERS013471_03025, ERS023446_03243, ERS024276_00059, ERS075361_03673, F6W99_02176, FRD82_16680, SAMEA2683035_03264
Production host: Rhodococcus jostii RHA1 (bacteria)
References: UniProt: A0A045J1S8, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop
Details: 15% w/v PEG4000, 0.2M ammonium acetate, 0.1M sodium citrate pH5.6

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.03→81.77 Å / Num. obs: 122908 / % possible obs: 93.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 30.45 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.2 / Net I/σ(I): 6.8
Reflection shellResolution: 2.03→2.31 Å / Rmerge(I) obs: 1.13 / Num. unique obs: 122908 / CC1/2: 0.665

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KZP

4kzp


Resolution: 2.03→81.77 Å / SU ML: 0.2619 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.5391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2498 2221 10.01 %
Rwork0.212 19972 -
obs0.2159 22193 57.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.91 Å2
Refinement stepCycle: LAST / Resolution: 2.03→81.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3865 0 0 108 3973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033934
X-RAY DIFFRACTIONf_angle_d0.485362
X-RAY DIFFRACTIONf_chiral_restr0.0491640
X-RAY DIFFRACTIONf_plane_restr0.0034708
X-RAY DIFFRACTIONf_dihedral_angle_d16.62171350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.120510.116310X-RAY DIFFRACTION0.48
2.08-2.130.2081120.2768112X-RAY DIFFRACTION5.36
2.13-2.180.2905190.2562168X-RAY DIFFRACTION7.95
2.18-2.240.228340.2336299X-RAY DIFFRACTION13.9
2.24-2.30.2584370.2712344X-RAY DIFFRACTION16.2
2.3-2.380.2436570.2654504X-RAY DIFFRACTION23.34
2.38-2.460.2627740.2572672X-RAY DIFFRACTION31.1
2.46-2.560.2891130.26661013X-RAY DIFFRACTION46.74
2.56-2.680.2841710.27341539X-RAY DIFFRACTION70.87
2.68-2.820.2972140.27211940X-RAY DIFFRACTION89.49
2.82-30.30712420.25272170X-RAY DIFFRACTION99.3
3-3.230.28242430.23282194X-RAY DIFFRACTION99.92
3.23-3.550.25382430.20092180X-RAY DIFFRACTION99.84
3.55-4.070.23062480.18012229X-RAY DIFFRACTION99.92
4.07-5.120.21922490.16742236X-RAY DIFFRACTION99.8
5.12-81.770.22382640.21132362X-RAY DIFFRACTION99.47

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