[English] 日本語
Yorodumi
- PDB-3i9s: Structure from the mobile metagenome of V.cholerae. Integron cass... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i9s
TitleStructure from the mobile metagenome of V.cholerae. Integron cassette protein VCH_CASS6
ComponentsIntegron cassette protein
KeywordsTRANSFERASE / Integron cassette protein / Vibrio cholerae / Oyster pond / Woods hole / Acetyltransferase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyGcn5-related N-acetyltransferase (GNAT) / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsDeshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / Xu, X. / Cui, H. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Chang, C. ...Deshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / Xu, X. / Cui, H. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Chang, C. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure from the mobile metagenome of V.cholerae. Integron cassette protein VCH_CASS6
Authors: Deshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / G Curmi, P.M. / Stokes, H.W. / Edwards, A. / Savchenko, A. / Mabbutt, B.C.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integron cassette protein
B: Integron cassette protein
C: Integron cassette protein
D: Integron cassette protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,64616
Polymers83,7364
Non-polymers91012
Water5,819323
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19420 Å2
ΔGint-241 kcal/mol
Surface area29410 Å2
MethodPISA
2
A: Integron cassette protein
B: Integron cassette protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2277
Polymers41,8682
Non-polymers3595
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-103 kcal/mol
Surface area16470 Å2
MethodPISA
3
C: Integron cassette protein
D: Integron cassette protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4199
Polymers41,8682
Non-polymers5517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-127 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.239, 75.239, 310.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11C-165-

SO4

21B-213-

HOH

31C-219-

HOH

41C-312-

HOH

DetailsPossible dimer/tetramer.

-
Components

#1: Protein
Integron cassette protein


Mass: 20933.939 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: OPVCH_OP3G / Gene: A59_A0465 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 294 K / pH: 6.5
Details: 0.1M Bis-tris, 1.5M NH4SO4, In situ proteolysis using 1/1000chymotrypsin. Cryo: paratone-N oil, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2008
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.2→52.44 Å / Num. all: 46726 / Num. obs: 46726 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.157 / Rsym value: 0.183 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.925 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6671 / Rsym value: 1.033 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.4_77)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→47.31 Å / SU ML: 0.34 / Isotropic thermal model: Isotropic / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 2152 4.62 %
Rwork0.183 --
obs0.185 46624 100 %
all-46624 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.9 Å2 / ksol: 0.35 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 44 323 5451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085229
X-RAY DIFFRACTIONf_angle_d0.9917026
X-RAY DIFFRACTIONf_dihedral_angle_d15.3251868
X-RAY DIFFRACTIONf_chiral_restr0.072761
X-RAY DIFFRACTIONf_plane_restr0.004882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25120.29131480.24212878X-RAY DIFFRACTION100
2.2512-2.30750.26931420.23132913X-RAY DIFFRACTION100
2.3075-2.36990.24351410.19712928X-RAY DIFFRACTION100
2.3699-2.43960.23151380.18442885X-RAY DIFFRACTION100
2.4396-2.51840.25181410.18232915X-RAY DIFFRACTION100
2.5184-2.60840.26141420.1842931X-RAY DIFFRACTION100
2.6084-2.71280.24571400.18742914X-RAY DIFFRACTION100
2.7128-2.83620.24031400.18582923X-RAY DIFFRACTION100
2.8362-2.98570.26111410.18772941X-RAY DIFFRACTION100
2.9857-3.17280.25771420.19492949X-RAY DIFFRACTION100
3.1728-3.41770.21681440.17282988X-RAY DIFFRACTION100
3.4177-3.76150.20471430.1582983X-RAY DIFFRACTION100
3.7615-4.30550.191450.13682994X-RAY DIFFRACTION100
4.3055-5.42320.19141480.14093077X-RAY DIFFRACTION100
5.4232-47.32520.23431570.20133253X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 42.9463 Å / Origin y: 0.1824 Å / Origin z: 134.6903 Å
111213212223313233
T0.2652 Å20.0042 Å2-0.1691 Å2-0.0357 Å20.0299 Å2--0.2747 Å2
L1.9896 °20.6608 °20.529 °2-0.9009 °2-0.1003 °2--1.3292 °2
S-0.282 Å °0.028 Å °0.5075 Å °-0.0826 Å °-0.0045 Å °0.2082 Å °-0.4021 Å °-0.048 Å °0.2873 Å °
Refinement TLS groupSelection details: CHAIN D

+
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