[English] 日本語
Yorodumi
- PDB-4rjk: Acetolactate synthase from Bacillus subtilis bound to LThDP - cry... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rjk
TitleAcetolactate synthase from Bacillus subtilis bound to LThDP - crystal form II
ComponentsAcetolactate synthase
KeywordsLYASE / ThDP
Function / homologyThiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PYRUVIC ACID / Chem-TDL / THIAMINE DIPHOSPHATE / :
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsSommer, B. / von Moeller, H. / Haack, M. / Qoura, F. / Langner, C. / Bourenkov, G. / Garbe, D. / Brueck, T. / Loll, B.
CitationJournal: Chembiochem / Year: 2015
Title: Detailed Structure-Function Correlations of Bacillus subtilis Acetolactate Synthase.
Authors: Sommer, B. / von Moeller, H. / Haack, M. / Qoura, F. / Langner, C. / Bourenkov, G. / Garbe, D. / Loll, B. / Bruck, T.
History
DepositionOct 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Jan 7, 2015Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetolactate synthase
B: Acetolactate synthase
C: Acetolactate synthase
D: Acetolactate synthase
E: Acetolactate synthase
F: Acetolactate synthase
G: Acetolactate synthase
H: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)509,77771
Polymers497,4948
Non-polymers12,28363
Water15,079837
1
A: Acetolactate synthase
B: Acetolactate synthase
C: Acetolactate synthase
D: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,01335
Polymers248,7474
Non-polymers6,26631
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33200 Å2
ΔGint-49 kcal/mol
Surface area65560 Å2
MethodPISA
2
E: Acetolactate synthase
F: Acetolactate synthase
hetero molecules

E: Acetolactate synthase
F: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,94842
Polymers248,7474
Non-polymers7,20138
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area35880 Å2
ΔGint-14 kcal/mol
Surface area65000 Å2
MethodPISA
3
G: Acetolactate synthase
H: Acetolactate synthase
hetero molecules

G: Acetolactate synthase
H: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,58130
Polymers248,7474
Non-polymers4,83426
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area31610 Å2
ΔGint-74 kcal/mol
Surface area65200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.510, 170.750, 342.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Acetolactate synthase /


Mass: 62186.750 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: PY79 / Gene: U712_18080 / Plasmid: pCBR / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: V5MX36, EC: 4.1.3.18

-
Non-polymers , 6 types, 900 molecules

#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H4O3
#6: Chemical ChemComp-TDL / 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-CARBOXY-1-HYDROXYETHYL)-5-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM / 2-LACTYLTHIAMIN DIPHOSPHATE


Mass: 513.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N4O10P2S
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 837 / 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: 3.28 Å3/Da / Density % sol: 62.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 45 % (v/v) PEG 200, 100 mM Tris/HCl, pH 7.0, 50 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2013
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 225545 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.3 % / Biso Wilson estimate: 47.7 Å2
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 14.2 % / % possible all: 100

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→29.997 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 21.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 11235 4.98 %RANDOM
Rwork0.1655 ---
obs0.1681 225424 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33774 0 701 837 35312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00935259
X-RAY DIFFRACTIONf_angle_d1.19247838
X-RAY DIFFRACTIONf_dihedral_angle_d15.31913154
X-RAY DIFFRACTIONf_chiral_restr0.0435447
X-RAY DIFFRACTIONf_plane_restr0.0056227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52840.28223730.20297103X-RAY DIFFRACTION100
2.5284-2.55810.28743750.20957096X-RAY DIFFRACTION100
2.5581-2.58930.27063720.20047096X-RAY DIFFRACTION100
2.5893-2.62210.30843740.20867051X-RAY DIFFRACTION100
2.6221-2.65650.2843700.21157076X-RAY DIFFRACTION100
2.6565-2.69290.26283680.20257021X-RAY DIFFRACTION100
2.6929-2.73140.27433740.19867110X-RAY DIFFRACTION100
2.7314-2.77210.28943730.19887064X-RAY DIFFRACTION100
2.7721-2.81540.27083670.18837051X-RAY DIFFRACTION100
2.8154-2.86150.27593770.19757125X-RAY DIFFRACTION100
2.8615-2.91080.26013710.18987074X-RAY DIFFRACTION100
2.9108-2.96370.2713710.18957068X-RAY DIFFRACTION100
2.9637-3.02060.25963740.19317133X-RAY DIFFRACTION100
3.0206-3.08220.26563720.18747108X-RAY DIFFRACTION100
3.0822-3.14920.24583690.18787058X-RAY DIFFRACTION100
3.1492-3.22240.2563730.19187126X-RAY DIFFRACTION100
3.2224-3.30290.24623750.18267127X-RAY DIFFRACTION100
3.3029-3.3920.23753750.17917119X-RAY DIFFRACTION100
3.392-3.49170.24023730.18217130X-RAY DIFFRACTION100
3.4917-3.60420.21573740.177129X-RAY DIFFRACTION100
3.6042-3.73280.22123740.16327135X-RAY DIFFRACTION100
3.7328-3.8820.21573760.15627141X-RAY DIFFRACTION100
3.882-4.05830.1963730.15297136X-RAY DIFFRACTION100
4.0583-4.27160.18983750.14927201X-RAY DIFFRACTION100
4.2716-4.53840.17863710.13637152X-RAY DIFFRACTION100
4.5384-4.88750.16863740.13467216X-RAY DIFFRACTION100
4.8875-5.37680.18163800.14537224X-RAY DIFFRACTION100
5.3768-6.1490.2133810.16217262X-RAY DIFFRACTION100
6.149-7.72510.19573850.15417322X-RAY DIFFRACTION100
7.7251-29.99870.15943960.14287535X-RAY DIFFRACTION99

+
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