[English] 日本語
Yorodumi
- PDB-2w1r: Crystal Structure of the C-terminal Domain of B. subtilis SpoVT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w1r
TitleCrystal Structure of the C-terminal Domain of B. subtilis SpoVT
ComponentsSTAGE V SPORULATION PROTEIN T
KeywordsTRANSCRIPTION / REGULATORY GAF DOMAIN OF SPOVT / TRANSCRIPTION REGULATION / REPRESSOR / ACTIVATOR / SPORULATION / DNA-BINDING
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / DNA binding / identical protein binding
Similarity search - Function
Sporulation stage V, protein T / Stage V sporulation protein T C-terminal, transcription factor / SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily / GAF domain / GAF-like domain superfamily / Beta-Lactamase ...Sporulation stage V, protein T / Stage V sporulation protein T C-terminal, transcription factor / SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Stage V sporulation protein T
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsAsen, I. / Djuranovic, S. / Lupas, A.N. / Zeth, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structure of Spovt, the Final Modulator of Gene Expression During Spore Development in Bacillus Subtilis
Authors: Asen, I. / Djuranovic, S. / Lupas, A.N. / Zeth, K.
History
DepositionOct 20, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: STAGE V SPORULATION PROTEIN T


Theoretical massNumber of molelcules
Total (without water)13,3971
Polymers13,3971
Non-polymers00
Water1,76598
1
A: STAGE V SPORULATION PROTEIN T

A: STAGE V SPORULATION PROTEIN T


Theoretical massNumber of molelcules
Total (without water)26,7942
Polymers26,7942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1450 Å2
ΔGint-16.1 kcal/mol
Surface area12960 Å2
MethodPQS
Unit cell
Length a, b, c (Å)63.930, 63.930, 77.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2044-

HOH

21A-2085-

HOH

-
Components

#1: Protein STAGE V SPORULATION PROTEIN T / SPOVT


Mass: 13396.901 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN GAF DOMAIN, RESIDUES 56-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: PY79 / Plasmid: PET30B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P37554
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAMINO ACIDS 55 - 178

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 55.2 % / Description: NONE
Crystal growpH: 7.5 / Details: 200 MM NACL, 100 MM HEPES PH 7.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.06→20 Å / Num. obs: 19148 / % possible obs: 97.8 % / Observed criterion σ(I): 4.7 / Redundancy: 11.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.3
Reflection shellResolution: 2.06→2.19 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.7 / % possible all: 91.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
XSCALEdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.364 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AMINO ACIDS AT THE N- AND C-TERMINUS WERE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.24217 1322 5.1 %RANDOM
Rwork0.22235 ---
obs0.22332 24815 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 0 98 983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022916
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.991.9661241
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0415122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.99625.71442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.315163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.839154
X-RAY DIFFRACTIONr_chiral_restr0.0650.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02689
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.2467
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.2654
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5941.5601
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0742945
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4753347
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3414.5293
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: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.349 98
Rwork0.328 1781

+
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