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- PDB-4yxt: PksG, a HMG-CoA Synthase from Bacillus subtilus -

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Basic information

Entry
Database: PDB / ID: 4yxt
TitlePksG, a HMG-CoA Synthase from Bacillus subtilus
ComponentsPolyketide biosynthesis 3-hydroxy-3-methylglutaryl-ACP synthase PksG
KeywordsTRANSFERASE / bacillaene / polyketide
Function / homology
Function and homology information


Transferases; Acyltransferases; Acyl groups converted into alkyl groups on transfer / hydroxymethylglutaryl-CoA synthase activity / acetyl-CoA metabolic process / antibiotic biosynthetic process / cytoplasm
Similarity search - Function
Hydroxymethylglutaryl-coenzyme A synthase, N-terminal / Hydroxymethylglutaryl-coenzyme A synthase, C-terminal domain / Hydroxymethylglutaryl-coenzyme A synthase N terminal / Hydroxymethylglutaryl-coenzyme A synthase C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-ACP synthase PksG
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsTill, M. / Nair, A.V. / Robson, A. / Race, P.R.
CitationJournal: To Be Published
Title: PksG, a HMG-CoA Synthase from Bacillus subtilus
Authors: Till, M. / Nair, A.V. / Robson, A. / Race, P.R.
History
DepositionMar 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-ACP synthase PksG
B: Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-ACP synthase PksG


Theoretical massNumber of molelcules
Total (without water)93,5422
Polymers93,5422
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-30 kcal/mol
Surface area29010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.160, 86.450, 107.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-ACP synthase PksG / HMG synthase


Mass: 46771.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: pksG, BSU17150 / Production host: Escherichia coli (E. coli)
References: UniProt: P40830, Transferases; Acyltransferases; Acyl groups converted into alkyl groups on transfer
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Morpheus screen A6 (molecular dimensions)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→64.7 Å / Num. obs: 60147 / % possible obs: 100 % / Redundancy: 10.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.232 / Rpim(I) all: 0.074 / Net I/σ(I): 7.4 / Num. measured all: 646983 / Scaling rejects: 171
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.9-1.949.72.5741.83712138420.8030.866100
9.11-64.710.20.05815.765226390.9780.0299.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.1.27data scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→64.7 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2609 / WRfactor Rwork: 0.2032 / FOM work R set: 0.8279 / SU B: 5.916 / SU ML: 0.156 / SU R Cruickshank DPI: 0.2602 / SU Rfree: 0.2111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 2247 5 %RANDOM
Rwork0.1976 ---
obs0.2005 42393 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.39 Å2 / Biso mean: 30.783 Å2 / Biso min: 12.65 Å2
Baniso -1Baniso -2Baniso -3
1--3.01 Å20 Å20 Å2
2---3.38 Å20 Å2
3---6.39 Å2
Refinement stepCycle: final / Resolution: 2.1→64.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6243 0 0 145 6388
Biso mean---29.93 -
Num. residues----806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196370
X-RAY DIFFRACTIONr_bond_other_d0.0010.025954
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9658598
X-RAY DIFFRACTIONr_angle_other_deg0.883313698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9715800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53423.659287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.354151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7831542
X-RAY DIFFRACTIONr_chiral_restr0.1030.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217258
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021480
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 170 -
Rwork0.256 3072 -
all-3242 -
obs--99.69 %

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