[English] 日本語
Yorodumi
- PDB-3dl3: Crystal structure of the tellurite resistance protein TehB. North... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dl3
TitleCrystal structure of the tellurite resistance protein TehB. Northeast Structural Genomics Consortium target VfR98 .
ComponentsTellurite resistance protein B
Keywordsstructural genomics / unknown function / X-Ray NESG VfR98 Q5E3X2_VIBF1 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyTellurite resistance predicted, YeaR / Domain of unknown function DUF1971 / TehB-like domain / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Tellurite resistance protein B
Function and homology information
Biological speciesVibrio fischeri ES114 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the tellurite resistance protein TehB. Northeast Structural Genomics Consortium target VfR98.
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJun 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tellurite resistance protein B
B: Tellurite resistance protein B
D: Tellurite resistance protein B
E: Tellurite resistance protein B
G: Tellurite resistance protein B
H: Tellurite resistance protein B
F: Tellurite resistance protein B
I: Tellurite resistance protein B


Theoretical massNumber of molelcules
Total (without water)111,6018
Polymers111,6018
Non-polymers00
Water1,51384
1
D: Tellurite resistance protein B

F: Tellurite resistance protein B


Theoretical massNumber of molelcules
Total (without water)27,9002
Polymers27,9002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area1900 Å2
ΔGint-17 kcal/mol
Surface area10220 Å2
MethodPISA
2
A: Tellurite resistance protein B

H: Tellurite resistance protein B


Theoretical massNumber of molelcules
Total (without water)27,9002
Polymers27,9002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1720 Å2
ΔGint-17 kcal/mol
Surface area9770 Å2
MethodPISA
3
B: Tellurite resistance protein B
E: Tellurite resistance protein B


Theoretical massNumber of molelcules
Total (without water)27,9002
Polymers27,9002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-16 kcal/mol
Surface area10330 Å2
MethodPISA
4
G: Tellurite resistance protein B
I: Tellurite resistance protein B


Theoretical massNumber of molelcules
Total (without water)27,9002
Polymers27,9002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-15 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.574, 205.020, 56.356
Angle α, β, γ (deg.)90.00, 110.21, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Tellurite resistance protein B


Mass: 13950.108 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri ES114 (bacteria) / Gene: tehB, VF_1779 / References: UniProt: Q5E3X2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 293 K / pH: 6
Details: 0.1M MgCl2 0.1M MES 40% PEG400, pH 6.0, Crystals were grown by microbatch under oil method. temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.979
SYNCHROTRONNSLS X4C2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 82534 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 19.6
Reflection shellResolution: 2.27→2.35 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.293

-
Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 320301.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3617 4.9 %RANDOM
Rwork0.232 ---
obs0.232 74329 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.9961 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 47.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.74 Å20 Å20.78 Å2
2---4.54 Å20 Å2
3---9.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6488 0 0 84 6572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 512 4.8 %
Rwork0.274 10102 -
obs--78.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

+
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