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- PDB-4yxq: PksG, a HMG-CoA Synthase from Bacillus subtilis -

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Basic information

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


Transferases; Acyltransferases; Acyl groups converted into alkyl groups on transfer / hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / acetyl-CoA metabolic process / ergosterol biosynthetic 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
DI(HYDROXYETHYL)ETHER / Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-ACP synthase PksG
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.47 Å
AuthorsNair, A.V. / Race, P.R. / Till, M.
CitationJournal: To Be Published
Title: PksG, a HMG-CoA Synthase from Bacillus subtilis
Authors: Nair, A.V. / Race, P.R. / Till, M.
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
C: Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-ACP synthase PksG
D: Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-ACP synthase PksG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,6357
Polymers187,3174
Non-polymers3183
Water6,431357
1
A: Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-ACP synthase PksG
B: Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-ACP synthase PksG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7643
Polymers93,6582
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-24 kcal/mol
Surface area27610 Å2
MethodPISA
2
C: Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-ACP synthase PksG
D: Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-ACP synthase PksG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8714
Polymers93,6582
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-21 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.620, 122.040, 198.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 2 - 420 / Label seq-ID: 2 - 420

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 46829.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: pksG, BSU17150 / Production host: Escherichia coli (E. coli)
References: UniProt: P40830, Transferases; Acyltransferases; Acyl groups converted into alkyl groups on transfer
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1 M MMT, 25% PEG 1500, 30% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.47→69.84 Å / Num. obs: 65451 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.253 / Rpim(I) all: 0.103 / Net I/σ(I): 6.2 / Num. measured all: 458826 / Scaling rejects: 1685
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
2.47-2.546.91.0651.93106945190.6830.436100
11.34-69.846.20.05812.849167900.9980.02499.2

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.47→63.74 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.861 / WRfactor Rfree: 0.2526 / WRfactor Rwork: 0.2096 / FOM work R set: 0.797 / SU B: 10.014 / SU ML: 0.223 / SU R Cruickshank DPI: 0.6604 / SU Rfree: 0.3124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.642 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 3310 5.1 %RANDOM
Rwork0.2258 ---
obs0.2281 62005 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.25 Å2 / Biso mean: 32.254 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20 Å2
2--0.56 Å20 Å2
3----2.13 Å2
Refinement stepCycle: final / Resolution: 2.47→63.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12560 0 21 357 12938
Biso mean--35.9 26.69 -
Num. residues----1618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01912834
X-RAY DIFFRACTIONr_bond_other_d0.0050.0211996
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.96517304
X-RAY DIFFRACTIONr_angle_other_deg1.01327602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38151608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77423.54582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.567152161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2571588
X-RAY DIFFRACTIONr_chiral_restr0.0970.21865
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114626
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023010
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A242670.05
12B242670.05
21A250320.04
22C250320.04
31A245650.03
32D245650.03
41B244670.05
42C244670.05
51B244300.04
52D244300.04
61C248010.03
62D248010.03
LS refinement shellResolution: 2.475→2.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 224 -
Rwork0.318 4528 -
all-4752 -
obs--99.98 %

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