[English] 日本語
Yorodumi
- PDB-3s7t: Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s7t
TitleCrystal structure of SeMet B. licheniformis CDPS YvmC-Blic
ComponentsPutative uncharacterized protein yvmC
KeywordsLIGASE / Rossmann Fold / tRNA / cyclodipeptide
Function / homology
Function and homology information


cyclo(L-leucyl-L-leucyl) synthase / pigment biosynthetic process / aminoacyltransferase activity
Similarity search - Function
Cyclodipeptide synthase / Cyclodipeptide synthase / Cyclodipeptide synthase / Cyclodipeptide synthase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cyclo(L-leucyl-L-leucyl) synthase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.808 Å
AuthorsBonnefond, L. / Ishitani, R. / Nureki, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog.
Authors: Bonnefond, L. / Arai, T. / Sakaguchi, Y. / Suzuki, T. / Ishitani, R. / Nureki, O.
History
DepositionMay 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein yvmC
B: Putative uncharacterized protein yvmC


Theoretical massNumber of molelcules
Total (without water)60,1702
Polymers60,1702
Non-polymers00
Water28816
1
A: Putative uncharacterized protein yvmC


Theoretical massNumber of molelcules
Total (without water)30,0851
Polymers30,0851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein yvmC


Theoretical massNumber of molelcules
Total (without water)30,0851
Polymers30,0851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.172, 54.713, 101.556
Angle α, β, γ (deg.)90.000, 130.050, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Putative uncharacterized protein yvmC / YvmC


Mass: 30084.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: ATCC 14580 / Gene: BL00817, BLi03566, yvmC / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2 / References: UniProt: Q65EX3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.65 Å3/Da / Density % sol: 53.65 % / Mosaicity: 0.389 ° / Mosaicity esd: 0.004 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 10000 14%, NaCl 100mM, 20% glycerol, pH 8.5, vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 15530 / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.148 / Χ2: 3.552 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.913.60.40115331.6611100
2.9-3.0213.60.35315401.839199.9
3.02-3.1513.60.28515521.9721100
3.15-3.3213.70.2315372.3851100
3.32-3.5313.60.18915243.0371100
3.53-3.813.50.1515533.721100
3.8-4.1813.40.11715644.3411100
4.18-4.79130.09815385.068199.8
4.79-6.0313.90.09715764.4891100
6.03-5013.30.07616136.958199.9

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SOLVEphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.808→38.871 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.86 / SU ML: 0.83 / σ(F): 0.13 / Phase error: 21.11 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2324 1519 9.9 %
Rwork0.1821 --
obs0.187 15342 97.76 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.351 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 116.69 Å2 / Biso mean: 25.8158 Å2 / Biso min: 8.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.8387 Å20 Å2-5.1876 Å2
2--0.1364 Å20 Å2
3----0.9751 Å2
Refinement stepCycle: LAST / Resolution: 2.808→38.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 0 16 3441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093520
X-RAY DIFFRACTIONf_angle_d1.2374770
X-RAY DIFFRACTIONf_chiral_restr0.101531
X-RAY DIFFRACTIONf_plane_restr0.006625
X-RAY DIFFRACTIONf_dihedral_angle_d15.0131274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.808-2.89860.27271140.20411093120785
2.8986-3.00210.32441330.19171236136997
3.0021-3.12230.24981390.20461234137398
3.1223-3.26430.24331370.18731261139898
3.2643-3.43630.23471440.17291272141699
3.4363-3.65150.21221400.16381263140399
3.6515-3.93320.21031360.169312831419100
3.9332-4.32850.19111400.16512571397100
4.3285-4.95380.22181410.15831302144399
4.9538-6.2370.23671450.22151285143099
6.237-38.87510.24621500.199213371487100

+
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