[English] 日本語
Yorodumi
- PDB-2q82: Crystal structure of core protein P7 from Pseudomonas phage phi12... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q82
TitleCrystal structure of core protein P7 from Pseudomonas phage phi12. Northeast Structural Genomics Target OC1
ComponentsCore protein P7
KeywordsSTRUCTURAL PROTEIN / P7 / core protein / NESG / OC1 / structural genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyOxidized Rhodanese; domain 1 - #20 / Core protein P7, N-terminal core domain / Oxidized Rhodanese; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / Core protein P7
Function and homology information
Biological speciesPseudomonas phage phi12 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83 Å
AuthorsBenach, J. / Eryilmaz, E. / Su, M. / Seetharaman, J. / Wei, H. / Gottlieb, P. / Hunt, J.F. / Ghose, R. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure and dynamics of the P7 protein from the bacteriophage phi 12.
Authors: Eryilmaz, E. / Benach, J. / Su, M. / Seetharaman, J. / Dutta, K. / Wei, H. / Gottlieb, P. / Hunt, J.F. / Ghose, R.
History
DepositionJun 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Oct 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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: Core protein P7


Theoretical massNumber of molelcules
Total (without water)14,4501
Polymers14,4501
Non-polymers00
Water3,387188
1
A: Core protein P7

A: Core protein P7


Theoretical massNumber of molelcules
Total (without water)28,9012
Polymers28,9012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area1350/11910
MethodPISA
Unit cell
Length a, b, c (Å)75.499, 75.499, 46.486
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe putative biological unit is a dimer, created by -x, -x+y, -z+2/3 + (1 1 0) symmetry operation

-
Components

#1: Protein Core protein P7


Mass: 14450.371 Da / Num. of mol.: 1 / Fragment: Residues 1-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phi12 (virus) / Genus: Cystovirus / Plasmid: pET21D / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q94M07
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 23% PEG10000, 100mM Sodium acetate, 10% n-Hexyl-D-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.97947 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 8, 2007 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionRedundancy: 10.5 % / Av σ(I) over netI: 12 / Number: 305699 / Rmerge(I) obs: 0.05 / Χ2: 0.78 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 29155 / % possible obs: 89.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.665098.410.0310.92111.6
2.913.6610010.0350.88611.6
2.542.9110010.0560.84711.6
2.312.5410010.090.80811.5
2.142.3110010.1250.77911.4
2.022.1499.810.190.71111.1
1.912.0295.710.2880.67910.3
1.831.9182.810.3880.6319.2
1.761.836910.4720.6047.5
1.71.7648.610.6740.6455.7
ReflectionResolution: 1.7→50 Å / Num. obs: 29155 / % possible obs: 89.4 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.7-1.765.70.67448.6
1.76-1.837.50.47269
1.83-1.919.20.38882.8
1.91-2.0210.30.28895.7
2.02-2.1411.10.1999.8
2.14-2.3111.40.125100
2.31-2.5411.50.09100
2.54-2.9111.60.056100
2.91-3.6611.60.035100
3.66-5011.60.03198.4

-
Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.88 Å / D res low: 5.83 Å / FOM : 0.295 / Reflection: 9638
Phasing MAD setR kraut acentric: 0.037 / Highest resolution: 5.83 Å / Lowest resolution: 1.88 Å / FOM : 0.297 / Power: 0.71 kW
Phasing dmFOM : 0.52 / FOM acentric: 0.52 / FOM centric: 0.5 / Reflection: 12613 / Reflection acentric: 11383 / Reflection centric: 1230
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.1-37.8890.920.950.84661494167
3.2-5.10.90.910.7919681697271
2.6-3.20.720.730.5823342108226
2.2-2.60.520.530.3622762090186
1.9-2.20.280.290.237983519279
1.8-1.90.130.130.0815761475101

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RESOLVE2.08phasing
CNS1.1refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.83→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflection
Rfree0.226 2070 7.9 %
Rwork0.21 --
obs0.21 21894 83.6 %
Solvent computationBsol: 52.745 Å2
Displacement parametersBiso mean: 39.389 Å2
Baniso -1Baniso -2Baniso -3
1-6.207 Å22.497 Å20 Å2
2--6.913 Å20 Å2
3----13.12 Å2
Refinement stepCycle: LAST / Resolution: 1.83→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms856 0 0 188 1044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used
1.83-1.850.214320.255270X-RAY DIFFRACTION41
1.85-1.860.32140.269254X-RAY DIFFRACTION41
1.86-1.880.359320.287280X-RAY DIFFRACTION41
1.88-1.890.278300.24308X-RAY DIFFRACTION41
1.89-1.910.236320.267310X-RAY DIFFRACTION41
1.91-1.930.235400.255374X-RAY DIFFRACTION41
1.93-1.950.318330.246342X-RAY DIFFRACTION41
1.95-1.970.314480.268395X-RAY DIFFRACTION41
1.97-1.990.198390.246404X-RAY DIFFRACTION41
1.99-2.010.312420.266387X-RAY DIFFRACTION41
2.01-2.030.252540.273456X-RAY DIFFRACTION41
2.03-2.050.296500.251464X-RAY DIFFRACTION41
2.05-2.080.298630.281474X-RAY DIFFRACTION41
2.08-2.10.253560.256490X-RAY DIFFRACTION41
2.1-2.130.279400.249464X-RAY DIFFRACTION41
2.13-2.160.195600.244526X-RAY DIFFRACTION41
2.16-2.190.309550.257479X-RAY DIFFRACTION41
2.19-2.220.191560.217569X-RAY DIFFRACTION41
2.22-2.250.242490.21500X-RAY DIFFRACTION41
2.25-2.290.227550.224525X-RAY DIFFRACTION41
2.29-2.320.286420.229502X-RAY DIFFRACTION41
2.32-2.360.213490.223518X-RAY DIFFRACTION41
2.36-2.410.243640.202520X-RAY DIFFRACTION41
2.41-2.450.314540.23540X-RAY DIFFRACTION41
2.45-2.50.336580.241532X-RAY DIFFRACTION41
2.5-2.560.278580.25507X-RAY DIFFRACTION41
2.56-2.620.199560.211563X-RAY DIFFRACTION41
2.62-2.680.226470.223547X-RAY DIFFRACTION41
2.68-2.750.278530.207532X-RAY DIFFRACTION41
2.75-2.840.284680.203545X-RAY DIFFRACTION41
2.84-2.930.203720.216534X-RAY DIFFRACTION41
2.93-3.030.237760.224555X-RAY DIFFRACTION41
3.03-3.150.28530.219580X-RAY DIFFRACTION41
3.15-3.290.238560.213578X-RAY DIFFRACTION41
3.29-3.470.184470.193558X-RAY DIFFRACTION41
3.47-3.680.147700.195570X-RAY DIFFRACTION41
3.68-3.970.18520.182592X-RAY DIFFRACTION41
3.97-4.360.19620.176562X-RAY DIFFRACTION41
4.36-4.980.172460.164585X-RAY DIFFRACTION41
4.98-6.250.26580.237570X-RAY DIFFRACTION41
6.25-200.211490.223563X-RAY DIFFRACTION41
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