[English] 日本語
Yorodumi
- PDB-1vaj: Crystal Structure of Uncharacterized Protein PH0010 From Pyrococc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vaj
TitleCrystal Structure of Uncharacterized Protein PH0010 From Pyrococcus horikoshii
ComponentsHypothetical protein PH0010
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha + beta fold
Function / homology
Function and homology information


Hypothetical protein ph0010; domain 2 / Hypothetical protein ph0010; domain 1 / AMMECR1 domain / Uncharacterised protein family MJ0810 / AMMECR1 / AMMECR1, N-terminal / AmmeMemoRadiSam system protein A / AMMECR1 domain superfamily / AMMECR1 / AMMECR1 domain profile. ...Hypothetical protein ph0010; domain 2 / Hypothetical protein ph0010; domain 1 / AMMECR1 domain / Uncharacterised protein family MJ0810 / AMMECR1 / AMMECR1, N-terminal / AmmeMemoRadiSam system protein A / AMMECR1 domain superfamily / AMMECR1 / AMMECR1 domain profile. / Glycoprotein, Type 4 Pilin / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.82 Å
AuthorsTajika, Y. / Sakai, N. / Tamura, T. / Yao, M. / Watanabe, N. / Tanaka, I.
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of PH0010 from Pyrococcus horikoshii, which is highly homologous to human AMMECR 1C-terminal region
Authors: Tajika, Y. / Sakai, N. / Tamura, T. / Yao, M. / Watanabe, N. / Tanaka, I.
History
DepositionFeb 17, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Hypothetical protein PH0010


Theoretical massNumber of molelcules
Total (without water)24,8621
Polymers24,8621
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.672, 67.223, 58.728
Angle α, β, γ (deg.)90.00, 104.27, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Hypothetical protein PH0010


Mass: 24862.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0010 / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli)
Strain (production host): BL21-codonplus(DE3)-RIL (Stratagene)
References: UniProt: O57770
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: PEG 8000, magnesium chloride, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9742, 0.9785, 0.9600
DetectorDetector: CCD / Date: Dec 21, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97421
20.97851
30.961
ReflectionResolution: 1.82→38.63 Å / Num. obs: 19449 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.6
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.336 / % possible all: 77.2

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.82→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1960 9.6 %RANDOM
Rwork0.202 ---
obs-19319 94.5 %-
Displacement parametersBiso mean: 20.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å21.56 Å2
2---4.21 Å20 Å2
3---5.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.82→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 0 165 1811
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcangle_it1.541
X-RAY DIFFRACTIONc_mcbond_it1.109
X-RAY DIFFRACTIONc_scangle_it2.963
X-RAY DIFFRACTIONc_scbond_it2.167
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_d23.54
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 1.82→1.88 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.314 132 9.6 %
Rwork0.302 1236 -
obs-1368 66.73 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.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://pdbjlvh1.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