[English] 日本語
Yorodumi
- PDB-4euy: Crystal structure of thioredoxin-like protein BCE_0499 from Bacil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4euy
TitleCrystal structure of thioredoxin-like protein BCE_0499 from Bacillus cereus ATCC 10987
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologyGlutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsShabalin, I.G. / Kagan, O. / Chruszcz, M. / Grabowski, M. / Savchenko, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of thioredoxin-like protein BCE_0499 from Bacillus cereus
Authors: Shabalin, I.G. / Kagan, O. / Chruszcz, M. / Grabowski, M. / Savchenko, A. / Joachimiak, A. / Minor, W.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,5321
Polymers12,5321
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.458, 73.458, 64.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

21A-205-

HOH

Detailsbiological unit is the same as asym. unit

-
Components

#1: Protein Uncharacterized protein


Mass: 12531.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: BCE_0499 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q73E61
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein: 0.3M NaCl, 10mM Hepes pH 7.5, 0.5 mM TCEP, Precipitant: 20% PEG3350, 0.2M tri-Li Citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2010 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 4254 / Num. obs: 4245 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Biso Wilson estimate: 111 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Χ2: 1.224 / Net I/σ(I): 41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
2.9-2.9513.90.8143.12063.10.705100
2.95-314.30.7541880.714100
3-3.06140.5262320.739100
3.06-3.1214.40.4641880.7100
3.12-3.1914.10.3052120.741100
3.19-3.2714.20.2462010.77100
3.27-3.3514.10.1842150.705100
3.35-3.4413.80.1621970.94100
3.44-3.5413.60.1262070.962100
3.54-3.65140.1042100.885100
3.65-3.7813.70.0932100.923100
3.78-3.9313.60.0772151.106100
3.93-4.1113.70.062060.967100
4.11-4.3313.70.0532181.133100
4.33-4.613.90.0412081.34100
4.6-4.9513.50.0462171.407100
4.95-5.4513.50.0612111.75599.1
5.45-6.2313.10.0742212.219100
6.23-7.8312.60.0742303.137100
7.83-3011.30.0692532.67897.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
MLPHAREphasing
CCP4phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2987 / WRfactor Rwork: 0.2122 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.807 / SU B: 30.558 / SU ML: 0.265 / SU R Cruickshank DPI: 0.4737 / SU Rfree: 0.3606 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.474 / ESU R Free: 0.361
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2962 194 4.6 %RANDOM
Rwork0.2195 ---
obs0.2227 4219 99.72 %-
all-4232 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 204.62 Å2 / Biso mean: 104.5937 Å2 / Biso min: 63.12 Å2
Baniso -1Baniso -2Baniso -3
1--7.36 Å20 Å20 Å2
2---7.36 Å20 Å2
3---14.72 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms677 0 0 9 686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02686
X-RAY DIFFRACTIONr_bond_other_d0.0010.02444
X-RAY DIFFRACTIONr_angle_refined_deg1.831.996929
X-RAY DIFFRACTIONr_angle_other_deg0.9483.0041087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.719584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4725.16131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81615115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.012153
X-RAY DIFFRACTIONr_chiral_restr0.0780.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02136
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 19 -
Rwork0.306 234 -
all-253 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
115.2672-3.48321.85679.0996-1.00788.2256-0.3781-0.31470.4232-0.8578-0.02150.0127-1.13550.40450.39950.55690.0686-0.06830.3739-0.02780.207725.04315.79625.815
29.6922-1.6286-1.88028.76373.98910.6893-0.0654-0.2038-0.3704-0.29690.14940.2621-0.2685-0.2615-0.0840.55290.0712-0.03290.40950.05720.258622.17710.98327.257
323.25495.792715.8669.422210.338622.44460.26221.123-0.1356-1.1532-0.09330.0807-0.560.7371-0.16880.787-0.01-0.06070.64870.01330.288128.7336.77417.488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 45
2X-RAY DIFFRACTION2A46 - 88
3X-RAY DIFFRACTION3A89 - 103

+
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