[English] 日本語
Yorodumi
- PDB-3oqj: Crystal structure of B. licheniformis CDPS yvmC-BLIC in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oqj
TitleCrystal structure of B. licheniformis CDPS yvmC-BLIC in complex with CAPSO
ComponentsPutative uncharacterized protein yvmC
KeywordsLIGASE / tRNA / ROSSMANN FOLD
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
Chem-3CX / Cyclo(L-leucyl-L-leucyl) synthase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.399 Å
AuthorsBonnefond, L. / Arai, T. / Suzuki, T. / 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
DepositionSep 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 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 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,8004
Polymers59,3262
Non-polymers4752
Water3,117173
1
A: Putative uncharacterized protein yvmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9002
Polymers29,6631
Non-polymers2371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein yvmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9002
Polymers29,6631
Non-polymers2371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.856, 54.713, 101.521
Angle α, β, γ (deg.)90.000, 130.440, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Putative uncharacterized protein yvmC / YvmC


Mass: 29662.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NdeI/XhoI restriction sites / 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: Chemical ChemComp-3CX / (2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid


Mass: 237.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.69 Å3/Da / Density % sol: 54.23 % / Mosaicity: 0.329 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 20% PEG 8000, pH 9.5, vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 5 % / Av σ(I) over netI: 21.73 / Number: 125460 / Rmerge(I) obs: 0.077 / Χ2: 1.09 / D res high: 2.399 Å / D res low: 50 Å / Num. obs: 24915 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.175010010.0341.3054.9
4.15.1710010.051.9634.8
3.584.110010.0481.1535.1
3.263.5810010.0670.9435.1
3.023.2610010.0980.8965.1
2.853.0210010.1350.9015.1
2.72.8510010.1840.9435.1
2.592.710010.2460.9645.1
2.492.5910010.3180.965.1
2.42.4910010.4010.9325
ReflectionResolution: 2.399→50 Å / Num. obs: 24915 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.077 / Χ2: 1.091 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.4950.40124920.9321100
2.49-2.595.10.31824690.961100
2.59-2.75.10.24624380.9641100
2.7-2.855.10.18424870.9431100
2.85-3.025.10.13524830.9011100
3.02-3.265.10.09824790.8961100
3.26-3.585.10.06724800.9431100
3.58-4.15.10.04824971.1531100
4.1-5.174.80.0525051.9631100
5.17-504.90.03425851.3051100

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å38.48 Å
Translation2.5 Å38.48 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.2.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.399→38.63 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8474 / SU ML: 0.32 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 1921 7.97 %
Rwork0.1781 --
obs0.1818 24116 96.55 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.409 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 99.38 Å2 / Biso mean: 32.6675 Å2 / Biso min: 13.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.2137 Å20 Å2-3.4427 Å2
2--2.7469 Å20 Å2
3----2.9606 Å2
Refinement stepCycle: LAST / Resolution: 2.399→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 30 173 3628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083525
X-RAY DIFFRACTIONf_angle_d1.0634763
X-RAY DIFFRACTIONf_chiral_restr0.074522
X-RAY DIFFRACTIONf_plane_restr0.004622
X-RAY DIFFRACTIONf_dihedral_angle_d13.6161299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3991-2.48490.28571630.21342061222489
2.4849-2.58440.26841900.20662098228893
2.5844-2.70190.26211850.19522129231494
2.7019-2.84440.25961870.19152187237495
2.8444-3.02250.24931950.18832223241897
3.0225-3.25580.26561940.18622240243498
3.2558-3.58320.23911970.17082283248099
3.5832-4.10120.20241980.16422982496100
4.1012-5.16510.17611990.150423082507100
5.1651-38.63520.2052130.18882368258199

+
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