[English] 日本語
Yorodumi
- PDB-3njc: Crystal structure of the yslB protein from Bacillus subtilis. Nor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3njc
TitleCrystal structure of the yslB protein from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR460.
ComponentsYSLB protein
Keywordsstructural genomics / unknown function / NESG / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyProtein of unknown function DUF2507 / Protein of unknown function (DUF2507) / Trafficking protein particle complex subunit 3 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / NO signalling/Golgi transport ligand-binding domain superfamily / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein YslB
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.693 Å
AuthorsVorobiev, S. / Abashidze, M. / Seetharaman, J. / Wang, D. / Cunningham, K. / Ma, L.-C. / Owens, L. / Fang, Y. / Xiao, R. / Acton, T.B. ...Vorobiev, S. / Abashidze, M. / Seetharaman, J. / Wang, D. / Cunningham, K. / Ma, L.-C. / Owens, L. / Fang, Y. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the yslB protein from Bacillus subtilis.
Authors: Vorobiev, S. / Abashidze, M. / Seetharaman, J. / Wang, D. / Cunningham, K. / Ma, L.-C. / Owens, L. / Fang, Y. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YSLB protein
B: YSLB protein


Theoretical massNumber of molelcules
Total (without water)37,8492
Polymers37,8492
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-49 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.827, 52.105, 136.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsdimer according to gel-filtration

-
Components

#1: Protein YSLB protein


Mass: 18924.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU28460, yslB / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: P42955
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18-20% PEG 4000, 0.1M HEPES, pH7.0, hanging drop at 291K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.693→500 Å / Num. obs: 71912 / % possible obs: 94.1 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.06 / Χ2: 1.528 / Net I/av σ(I): 37.226 / Net I/σ(I): 15.7 / Num. measured all: 495994
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.765.80.36970400.90191.5
1.76-1.835.80.29969320.95391.3
1.83-1.915.70.21470191.06591.5
1.91-2.025.60.15370331.22692
2.02-2.145.60.1270671.41393
2.14-2.315.50.09572931.56295.6
2.31-2.545.60.08174881.65498.1
2.54-2.919.10.06775931.76299
2.91-3.6610.30.05274931.90898.4
3.66-5009.60.04569541.90590.8

-
Processing

Software
NameVersionClassification
SHELXDEphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementResolution: 1.693→28.207 Å / SU ML: 0.26 / σ(F): 1.21 / Phase error: 24.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 3604 5.02 %
Rwork0.1851 --
obs0.1875 71835 93.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.391 Å2 / ksol: 0.402 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.9613 Å20 Å2-0 Å2
2--10.7284 Å2-0 Å2
3----6.4649 Å2
Refinement stepCycle: LAST / Resolution: 1.693→28.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 0 186 2631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062509
X-RAY DIFFRACTIONf_angle_d13380
X-RAY DIFFRACTIONf_dihedral_angle_d17.963924
X-RAY DIFFRACTIONf_chiral_restr0.075349
X-RAY DIFFRACTIONf_plane_restr0.005434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6931-1.71540.28641280.20462280X-RAY DIFFRACTION80
1.7154-1.73890.24371160.18132530X-RAY DIFFRACTION91
1.7389-1.76370.27271420.18342566X-RAY DIFFRACTION91
1.7637-1.790.2911470.18632574X-RAY DIFFRACTION92
1.79-1.8180.2631100.17662527X-RAY DIFFRACTION90
1.818-1.84780.24581540.16792582X-RAY DIFFRACTION91
1.8478-1.87960.25431410.17312508X-RAY DIFFRACTION92
1.8796-1.91380.24921240.17912613X-RAY DIFFRACTION92
1.9138-1.95060.261330.17012584X-RAY DIFFRACTION92
1.9506-1.99040.21061410.16642593X-RAY DIFFRACTION92
1.9904-2.03370.23321180.15962541X-RAY DIFFRACTION92
2.0337-2.0810.24421200.14922670X-RAY DIFFRACTION93
2.081-2.1330.21941280.15612617X-RAY DIFFRACTION94
2.133-2.19060.20991270.15812658X-RAY DIFFRACTION95
2.1906-2.25510.21791340.16372708X-RAY DIFFRACTION96
2.2551-2.32780.2621350.16092710X-RAY DIFFRACTION97
2.3278-2.4110.211390.16582729X-RAY DIFFRACTION98
2.411-2.50750.2471280.16852805X-RAY DIFFRACTION99
2.5075-2.62150.27271220.1822782X-RAY DIFFRACTION98
2.6215-2.75960.24771330.18382812X-RAY DIFFRACTION100
2.7596-2.93230.21191730.1862729X-RAY DIFFRACTION99
2.9323-3.15850.22421610.20362734X-RAY DIFFRACTION99
3.1585-3.47580.18761730.17832732X-RAY DIFFRACTION98
3.4758-3.97760.16741510.17872702X-RAY DIFFRACTION97
3.9776-5.00680.1971720.16022575X-RAY DIFFRACTION93
5.0068-28.21050.27511540.21552370X-RAY DIFFRACTION86

+
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://pdbjlvh1.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