[English] 日本語
Yorodumi
- PDB-4yxv: PksG, a HMG-CoA Synthase from Bacillus subtilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yxv
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: 2.75 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 1.1Jan 10, 2024Group: 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)93,5942
Polymers93,5942
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-31 kcal/mol
Surface area27980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.668, 123.632, 199.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21B-501-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / 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-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

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


Mass: 46797.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20 % w/v PEG 3350, 0.2 M sodium citrate, 0.1 M Bis Tris propane
PH range: 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / 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: 2.6→66.45 Å / Num. obs: 28839 / % possible obs: 100 % / Redundancy: 5.5 % / CC1/2: 0.922 / Rmerge(I) obs: 0.475 / Rpim(I) all: 0.22 / Net I/σ(I): 5.9 / Num. measured all: 157947 / Scaling rejects: 1045
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all
2.6-2.725.71.4720.61967734720.7130.673
9.01-66.454.40.18136.534077760.9520.094

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.1.27data scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YXQ

4yxq


Resolution: 2.75→64 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2609 / WRfactor Rwork: 0.221 / FOM work R set: 0.8459 / SU B: 13.204 / SU ML: 0.262 / SU Rfree: 0.3513 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 1243 5.1 %RANDOM
Rwork0.1906 ---
obs0.1931 23142 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: 146.31 Å2 / Biso mean: 49.919 Å2 / Biso min: 16.23 Å2
Baniso -1Baniso -2Baniso -3
1-2.8 Å20 Å20 Å2
2--4.45 Å20 Å2
3----7.26 Å2
Refinement stepCycle: final / Resolution: 2.75→64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6223 0 0 41 6264
Biso mean---39.94 -
Num. residues----799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196352
X-RAY DIFFRACTIONr_bond_other_d0.0040.025963
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9658566
X-RAY DIFFRACTIONr_angle_other_deg0.965313711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50623.507288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.658151076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4661543
X-RAY DIFFRACTIONr_chiral_restr0.0870.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217222
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021495
Refine LS restraints NCS

Ens-ID: 1 / Number: 24007 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.75→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 85 -
Rwork0.319 1675 -
all-1760 -
obs--99.77 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more