[English] 日本語
Yorodumi
- PDB-4ug3: B. subtilis GpsB N-terminal Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ug3
TitleB. subtilis GpsB N-terminal Domain
ComponentsCELL CYCLE PROTEIN GPSB
KeywordsCELL CYCLE / BACTERIAL GROWTH REGULATION / CELL WALL SYNTHESIS / CELL DIVISION
Function / homologyCell cycle protein GpsB / DivIVA family / DivIVA domain / DivIVA protein / regulation of cell shape / cell cycle / cell division / cytoplasm / Cell cycle protein GpsB
Function and homology information
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRismondo, J. / Cleverley, R.M. / Lane, H.V. / Grohennig, S. / Steglich, A. / Moller, L. / Krishna Mannala, G. / Hain, T. / Lewis, R.J. / Halbedel, S.
CitationJournal: Mol.Microbiol. / Year: 2016
Title: Structure of the Bacterial Cell Division Determinant Gpsb and its Interaction with Penicillin Binding Proteins.
Authors: Rismondo, J. / Cleverley, R.M. / Lane, H.V. / Grosshennig, S. / Steglich, A. / Moller, L. / Mannala, G.K. / Hain, T. / Lewis, R.J. / Halbedel, S.
History
DepositionMar 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CELL CYCLE PROTEIN GPSB
B: CELL CYCLE PROTEIN GPSB
C: CELL CYCLE PROTEIN GPSB
D: CELL CYCLE PROTEIN GPSB


Theoretical massNumber of molelcules
Total (without water)33,6544
Polymers33,6544
Non-polymers00
Water362
1
A: CELL CYCLE PROTEIN GPSB
B: CELL CYCLE PROTEIN GPSB


Theoretical massNumber of molelcules
Total (without water)16,8272
Polymers16,8272
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-35.9 kcal/mol
Surface area9140 Å2
MethodPISA
2
C: CELL CYCLE PROTEIN GPSB
D: CELL CYCLE PROTEIN GPSB


Theoretical massNumber of molelcules
Total (without water)16,8272
Polymers16,8272
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-32.5 kcal/mol
Surface area7260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.672, 39.893, 77.277
Angle α, β, γ (deg.)90.00, 103.28, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
CELL CYCLE PROTEIN GPSB / / GUIDING PBP1-SHUTTLING PROTEIN / GPSB


Mass: 8413.601 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 1-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CI74
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.31 Å3/Da / Density % sol: 46.72 % / Description: NONE
Crystal growpH: 6.5
Details: 0.05M BIS TRIS PH 6.5, 0.05M AMMONIUM SULPHATE, 30% PENTAERYTHRITOL ETHOXYLATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2015
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→50.3 Å / Num. obs: 7791 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UG1

4ug1


Resolution: 2.8→50.3 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.848 / SU B: 17.384 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.30114 801 10.3 %RANDOM
Rwork0.21626 ---
obs0.2245 6984 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.503 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-0.13 Å2
2--0.09 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 0 2 1946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191965
X-RAY DIFFRACTIONr_bond_other_d0.0010.021951
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9862611
X-RAY DIFFRACTIONr_angle_other_deg0.88134539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5785226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.54326.944108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.02715443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.529154
X-RAY DIFFRACTIONr_chiral_restr0.0750.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02398
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1725.09916
X-RAY DIFFRACTIONr_mcbond_other3.1735.087915
X-RAY DIFFRACTIONr_mcangle_it4.9057.6141138
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6295.4771049
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 58 -
Rwork0.259 524 -
obs--99.66 %

+
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