[English] 日本語
Yorodumi
- PDB-2eh1: Stage V Sporolation Protein S (SpoVS) from Thermus thermophilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2eh1
TitleStage V Sporolation Protein S (SpoVS) from Thermus thermophilus
ComponentsStage V sporulation protein S (SpoVS) related protein
KeywordsCELL CYCLE / Sporulation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


nucleic acid binding / metal ion binding
Similarity search - Function
Sporulation stage V, protein S / Stage V sporulation protein S (SpoVS) / Alba-like domain / Alba-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Stage V sporulation protein S (SpoVS) related protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsRehse, P.H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Stage V Sporolation Protein S (SpoVS) from Thermus thermophilus
Authors: Rehse, P.H. / Yokoyama, S.
History
DepositionMar 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Stage V sporulation protein S (SpoVS) related protein
B: Stage V sporulation protein S (SpoVS) related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,06310
Polymers19,5782
Non-polymers4858
Water1,31573
1
A: Stage V sporulation protein S (SpoVS) related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9734
Polymers9,7891
Non-polymers1833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Stage V sporulation protein S (SpoVS) related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0916
Polymers9,7891
Non-polymers3025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Stage V sporulation protein S (SpoVS) related protein
hetero molecules

B: Stage V sporulation protein S (SpoVS) related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,06310
Polymers19,5782
Non-polymers4858
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_664-x+y+1,-x+1,z-1/31
Buried area2730 Å2
ΔGint-80 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.778, 71.778, 80.833
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Stage V sporulation protein S (SpoVS) related protein


Mass: 9789.034 Da / Num. of mol.: 2 / Mutation: L22MSE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q5SK02
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 100mM Imidazole, 25% propylene glycol, 200mM Zinc Acetate, 10% glycerol, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97896, 0.97926, 0.9000
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 2, 2006 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978961
20.979261
30.91
Reflection

D res high: 2.25 Å / D res low: 50 Å / % possible obs: 99.9

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs
10.4119.81237750.081.0511861
10216.61193690.082111942
10.4317.61238910.0770.9911912
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.855099.510.071.0839.2
3.854.8510010.061.0310.2
3.363.8510010.0641.08410.4
3.053.3610010.0781.00610.6
2.833.0510010.0930.99310.6
2.672.8310010.1061.04310.6
2.532.6710010.1291.04210.7
2.422.5310010.1511.07610.7
2.332.4210010.181.06710.7
2.252.3310010.2191.04410.7
4.855099.620.0591.0759.2
3.854.8510020.0561.08510.2
3.363.8510020.0630.92610.4
3.053.3610020.0840.97210.5
2.833.0510020.1141.02310.6
2.672.8310020.1451.03410.7
2.532.6710020.2021.03410.7
2.422.5310020.2490.9710.4
2.332.4299.820.3030.9089.5
2.252.3399.320.40.8887.7
4.855099.430.0591.0139.2
3.854.8510030.0561.06310.1
3.363.8510030.061.17210.4
3.053.3610030.0750.91510.5
2.833.0510030.0950.93410.6
2.672.8310030.1140.98610.6
2.532.6710030.1460.97810.7
2.422.5310030.1750.98110.7
2.332.4210030.2140.9710.7
2.252.3310030.2660.91610.5
ReflectionResolution: 2.25→50 Å / Num. all: 11861 / Num. obs: 11861 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.08 / Χ2: 1.047 / Net I/σ(I): 19.8
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 12.8 / Num. unique all: 1145 / Χ2: 1.044 / % possible all: 100

-
Phasing

Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 11817
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.69-10061.70.822502
5.27-6.6958.50.919502
4.56-5.2757.10.94507
4.12-4.5655.90.948509
3.82-4.12600.935508
3.58-3.8258.30.933506
3.4-3.5858.70.932509
3.25-3.462.20.925508
3.11-3.2560.90.915507
3-3.11610.913509
2.91-360.10.919517
2.82-2.9167.20.91514
2.74-2.8265.10.888512
2.68-2.7468.30.909512
2.61-2.6872.60.908503
2.56-2.6168.40.901520
2.5-2.5670.80.91531
2.45-2.571.50.884532
2.4-2.45770.883543
2.36-2.475.50.908569
2.31-2.3677.60.896550
2.25-2.3182.60.816947

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
DM5phasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→33.9 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1060 4.8 %random
Rwork0.199 ---
all0.199 11803 --
obs0.199 11803 98.4 %-
Solvent computationBsol: 48.828 Å2
Displacement parametersBiso mean: 32.709 Å2
Baniso -1Baniso -2Baniso -3
1--3.298 Å2-2.835 Å20 Å2
2---3.298 Å20 Å2
3---6.596 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.25→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 26 73 1432
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0086221.5
X-RAY DIFFRACTIONc_angle_deg1.554422
X-RAY DIFFRACTIONc_dihedral_angle_d24.394912
X-RAY DIFFRACTIONc_improper_angle_d0.885082.5
LS refinement shellResolution: 2.25→2.33 Å
RfactorNum. reflection% reflection
Rfree0.2539 86 -
Rwork0.1972 --
obs-2114 96.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4act.param

+
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