[English] 日本語
Yorodumi
- PDB-3bb6: Crystal structure of the P64488 protein from E.coli (strain K12).... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bb6
TitleCrystal structure of the P64488 protein from E.coli (strain K12). Northeast Structural Genomics Consortium target ER596
ComponentsUncharacterized protein yeaR
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / P64488 / ER596 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyTellurite resistance predicted, YeaR / Domain of unknown function DUF1971 / Domain of unknown function (DUF1971) / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein YeaR
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Janjua, H. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Janjua, H. / Owens, L. / Ma, L.-C. / 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: X-Ray structure of the P64488 from E.coli (strain K12).
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Janjua, H. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein yeaR
B: Uncharacterized protein yeaR
C: Uncharacterized protein yeaR
D: Uncharacterized protein yeaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8108
Polymers59,5494
Non-polymers2624
Water3,333185
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
MethodPISA
2
A: Uncharacterized protein yeaR
C: Uncharacterized protein yeaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9054
Polymers29,7742
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
MethodPISA
3
B: Uncharacterized protein yeaR
D: Uncharacterized protein yeaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9054
Polymers29,7742
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.943, 82.472, 109.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Uncharacterized protein yeaR


Mass: 14887.153 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yeaR, b1797, JW1786 / Production host: Escherichia coli (E. coli) / References: UniProt: P64488
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 53.12 %
Crystal growTemperature: 293 K / pH: 5.2
Details: PEG 8000, 0.1M NaNO3, 0.1M MES, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 2007
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: 51838 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.9
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 3.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 87541.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: THE FRIEDEL PAIRS WERE USED IN PHASING. BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2377 4.4 %RANDOM
Rwork0.219 ---
obs0.219 48327 85.1 %-
all-48327 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.27 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-9.578 Å20 Å20 Å2
2---2.746 Å20 Å2
3----6.832 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3527 0 4 185 3716
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4131.5
X-RAY DIFFRACTIONc_mcangle_it2.3332
X-RAY DIFFRACTIONc_scbond_it2.2692
X-RAY DIFFRACTIONc_scangle_it3.3062.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 295 4.8 %
Rwork0.261 5896 -
obs--69.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.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