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- PDB-7lgb: ChsB1 in complex with NAD+ -

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Basic information

Entry
Database: PDB / ID: 7lgb
TitleChsB1 in complex with NAD+
Components3-ketoacyl-ACP reductase
KeywordsOXIDOREDUCTASE / short-chain type alcohol dehydrogenase/reductase hydroxyacyl-CoA dehydrogenase
Function / homology
Function and homology information


3-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
Similarity search - Function
: / : / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-ketoacyl-ACP reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4282
Polymers32,7651
Non-polymers6631
Water1,74797
1
A: 3-ketoacyl-ACP reductase
hetero molecules

A: 3-ketoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8564
Polymers65,5292
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9430 Å2
ΔGint-63 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.662, 84.233, 47.341
Angle α, β, γ (deg.)90.000, 116.188, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 32764.697 Da / Num. of mol.: 1
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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium citrate, 0.1M HEPES pH7.5, 30% v/v 2-methyl-2,4-pentanediol

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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: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.21→42.48 Å / Num. obs: 103397 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 29.24 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.4
Reflection shellResolution: 2.21→2.25 Å / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 103397 / CC1/2: 0.739

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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: 2.21→42.48 Å / SU ML: 0.2271 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.7343
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2074 1506 10 %
Rwork0.1666 13549 -
obs0.1707 15055 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.56 Å2
Refinement stepCycle: LAST / Resolution: 2.21→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 44 97 2159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01382144
X-RAY DIFFRACTIONf_angle_d0.93482938
X-RAY DIFFRACTIONf_chiral_restr0.0895351
X-RAY DIFFRACTIONf_plane_restr0.0043374
X-RAY DIFFRACTIONf_dihedral_angle_d22.0557732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.280.26351370.19761230X-RAY DIFFRACTION100
2.28-2.360.24371370.1851229X-RAY DIFFRACTION99.93
2.36-2.450.23921330.17721205X-RAY DIFFRACTION100
2.45-2.570.23131380.16911236X-RAY DIFFRACTION100
2.57-2.70.23241370.16991234X-RAY DIFFRACTION100
2.7-2.870.22141350.17091224X-RAY DIFFRACTION99.93
2.87-3.090.21031360.16111223X-RAY DIFFRACTION100
3.09-3.40.21791370.15391224X-RAY DIFFRACTION99.85
3.4-3.890.18411370.14841232X-RAY DIFFRACTION100
3.89-4.910.14541380.14251247X-RAY DIFFRACTION99.93
4.91-42.480.23641410.1981265X-RAY DIFFRACTION99.86

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