[English] 日本語
Yorodumi
- PDB-3gw4: Crystal structure of uncharacterized protein from Deinococcus rad... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gw4
TitleCrystal structure of uncharacterized protein from Deinococcus radiodurans. Northeast Structural Genomics Consortium Target DrR162B.
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / DrR162B
Function / homologyTetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.49 Å
AuthorsKuzin, A.P. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. ...Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Northeast Structural Genomics Consortium Target DrR162B
Authors: Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)45,9412
Polymers45,9412
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-23 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.850, 70.680, 102.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Uncharacterized protein


Mass: 22970.680 Da / Num. of mol.: 2 / Fragment: UNP residues 14-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: R1 / DSM 20539 / IFO 15346 / LMG 4051 / NCIB 9279 / Gene: DR_2358 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9RRX4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl pH 7.5. Reservoir solution: 1.9M Na-malonate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97914, 0.97928, 0.96784
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2009 / Details: mirrors
RadiationMonochromator: Si(111) CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979141
20.979281
30.967841
ReflectionResolution: 2.49→50 Å / Num. obs: 15135 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 25.4
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 6.7 / Num. unique all: 1474 / % possible all: 98.5

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.49→19.43 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.896 / SU B: 23.961 / SU ML: 0.241 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.872 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.264 729 5.1 %RANDOM
Rwork0.225 ---
obs0.227 14352 100 %-
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 mean: 26.433 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.49→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 0 23 3073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213108
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9334201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8525387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03624.19179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.91615500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7511528
X-RAY DIFFRACTIONr_chiral_restr0.0870.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022477
X-RAY DIFFRACTIONr_nbd_refined0.2150.21453
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22137
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2960.24
X-RAY DIFFRACTIONr_mcbond_it0.8891.51984
X-RAY DIFFRACTIONr_mcangle_it1.19823020
X-RAY DIFFRACTIONr_scbond_it1.87631261
X-RAY DIFFRACTIONr_scangle_it2.9524.51181
LS refinement shellResolution: 2.49→2.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 48 -
Rwork0.261 799 -
obs-847 100 %
Refinement TLS params.Method: refined / Origin x: 1.474 Å / Origin y: 4.6043 Å / Origin z: 12.6935 Å
111213212223313233
T0.1929 Å20.0188 Å20.0124 Å2-0.1213 Å20.0571 Å2--0.2195 Å2
L1.4282 °20.814 °2-0.8337 °2-0.5184 °2-0.5042 °2--0.5021 °2
S0.0514 Å °-0.3073 Å °-0.3564 Å °0.1399 Å °0.0367 Å °-0.0201 Å °0.0056 Å °-0.0238 Å °-0.0881 Å °

+
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