[English] 日本語
Yorodumi
- PDB-2oka: Crystal structure of Q9HYQ7_PSEAE from Pseudomonas aeruginosa. No... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2oka
TitleCrystal structure of Q9HYQ7_PSEAE from Pseudomonas aeruginosa. Northeast Structural Genomics Consortium target PaR82
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / par82 / nesg / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologySelenoprotein, Rdx-type / Rdx family / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / SelT/SelW/SelH family protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBenach, J. / Neely, H. / Seetharaman, J. / Chen, X.C. / Fang, Y. / Cunningham, K. / Owens, L. / Ma, L.C. / Xiao, R. / Liu, J. ...Benach, J. / Neely, H. / Seetharaman, J. / Chen, X.C. / Fang, Y. / Cunningham, K. / Owens, L. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of Q9HYQ7_PSEAE from Pseudomonas aeruginosa
Authors: Benach, J. / Neely, H. / Seetharaman, J. / Chen, X.C. / Fang, Y. / Cunningham, K. / Owens, L. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJan 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
D: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)47,5944
Polymers47,5944
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-27 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.161, 81.421, 92.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe AU contains one biological assembly. A tetramer

-
Components

#1: Protein
Hypothetical protein


Mass: 11898.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3338 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9HYQ7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 278 K / Method: microbatch under oil / pH: 6
Details: 0.1M MgSO4, 0.1M MES pH 6.0, 40% PEG 400. Drop: 2 microliter protein plus 1 microliter mother liquid, mineral oil, MICROBATCH UNDER OIL, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 14.6 / Number: 99685 / Rmerge(I) obs: 0.065 / Χ2: 0.78 / D res high: 2.5 Å / D res low: 20 Å / Num. obs: 27010 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.52.5994.210.3630.5892.6
2.592.6999.210.3110.6013.5
2.692.8110010.2670.5553.9
2.812.9610010.1790.5513.9
2.963.1510010.1120.5943.9
3.153.3910010.0810.6373.9
3.393.7399.410.0590.83.8
3.734.2610010.0450.8143.9
4.265.3510010.0471.3953.8
5.352099.910.0351.1663.8
ReflectionResolution: 2.5→20 Å / Num. obs: 27010 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Χ2: 0.78 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.592.60.36325640.58994.2
2.59-2.693.50.31127050.60199.2
2.69-2.813.90.26727020.555100
2.81-2.963.90.17927260.551100
2.96-3.153.90.11227290.594100
3.15-3.393.90.08127120.637100
3.39-3.733.80.05927010.899.4
3.73-4.263.90.04527180.814100
4.26-5.353.80.04727351.395100
5.35-203.80.03527181.16699.9

-
Phasing

Phasing MRRfactor: 36.2 / Cor.coef. Fo:Fc: 66.46
Highest resolutionLowest resolution
Rotation3 Å10 Å
Translation3 Å10 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
COMO1.2phasing
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OBK

2obk


Resolution: 2.5→20 Å / FOM work R set: 0.847 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflection
Rfree0.252 2333 8.5 %
Rwork0.217 --
obs0.217 24956 91.4 %
Solvent computationBsol: 29.481 Å2
Displacement parametersBiso mean: 47.532 Å2
Baniso -1Baniso -2Baniso -3
1--6.991 Å20 Å20 Å2
2--10.478 Å20 Å2
3----3.488 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 0 104 2756
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it4.7951.5
X-RAY DIFFRACTIONc_scbond_it4.2312
X-RAY DIFFRACTIONc_mcangle_it6.7152
X-RAY DIFFRACTIONc_scangle_it7.6622.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 46

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.5-2.520.213170.23302319
2.52-2.540.184350.223389424
2.54-2.560.297590.27387446
2.56-2.580.279480.24390438
2.58-2.60.238450.289419464
2.6-2.620.229370.237425462
2.62-2.640.267750.226443518
2.64-2.660.325560.287378434
2.66-2.690.276390.238481520
2.69-2.710.269580.25479537
2.71-2.740.294370.295450487
2.74-2.760.402550.273445500
2.76-2.790.302490.293522571
2.79-2.820.384470.271454501
2.82-2.850.42580.253477535
2.85-2.880.243760.236466542
2.88-2.910.416520.298490542
2.91-2.950.288350.242479514
2.95-2.980.341690.245516585
2.98-3.020.292470.255499546
3.02-3.060.334400.235536576
3.06-3.10.317500.243510560
3.1-3.150.265600.255513573
3.15-3.190.308430.267506549
3.19-3.240.277690.276507576
3.24-3.30.213530.252509562
3.3-3.350.315520.217540592
3.35-3.410.254480.234531579
3.41-3.480.299570.238518575
3.48-3.550.285600.26528588
3.55-3.630.286550.208534589
3.63-3.710.174510.189491542
3.71-3.80.231370.193541578
3.8-3.910.221460.194554600
3.91-4.020.229480.205520568
4.02-4.150.163480.183551599
4.15-4.290.185600.183526586
4.29-4.470.187460.175556602
4.47-4.670.21530.146526579
4.67-4.910.229370.174553590
4.91-5.210.223510.201527578
5.21-5.60.293640.204530594
5.6-6.150.291470.238539586
6.15-7.010.269580.238514572
7.01-8.710.175490.186540589
8.71-200.182570.194532589
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.par
X-RAY DIFFRACTION2water_rep.param

+
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