[English] 日本語
Yorodumi
- PDB-1wu8: Crystal structure of project PH0463 from Pyrococcus horikoshii OT3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wu8
TitleCrystal structure of project PH0463 from Pyrococcus horikoshii OT3
Componentshypothetical protein PH0463
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


(R)-S-adenosyl-L-methionine hydrolase (adenosine-forming) / hydrolase activity
Similarity search - Function
Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase N-terminal domain / SAM hydroxide adenosyltransferase C-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 ...Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase N-terminal domain / SAM hydroxide adenosyltransferase C-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / (R)-S-adenosyl-L-methionine hydrolase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsShimizu, K. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of project ID PH0463 from Pyrococcus horikoshii OT3
Authors: Shimizu, K. / Kunishima, N.
History
DepositionDec 2, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein PH0463
B: hypothetical protein PH0463
C: hypothetical protein PH0463
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6026
Polymers86,8013
Non-polymers8023
Water4,918273
1
A: hypothetical protein PH0463
B: hypothetical protein PH0463
C: hypothetical protein PH0463
hetero molecules

A: hypothetical protein PH0463
B: hypothetical protein PH0463
C: hypothetical protein PH0463
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,20512
Polymers173,6016
Non-polymers1,6036
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-38 kcal/mol
Surface area28290 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)138.756, 138.756, 139.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
DetailsThe biological assembly is a dimer.

-
Components

#1: Protein hypothetical protein PH0463


Mass: 28933.562 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58212
#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 3.9 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 291 K / Method: microbach / pH: 5.9
Details: 44 v/v (%) MPD, 0.1M Citr., 10M Dioxane, pH 5.9, Microbach, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.979056 Å
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Jun 29, 2004 / Details: Mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979056 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 42753 / Num. obs: 42753 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Biso Wilson estimate: 56.9 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.093 / Net I/σ(I): 8.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.404 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→38.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1937651.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2090 4.9 %RANDOM
Rwork0.195 ---
obs0.195 42530 99.9 %-
all-42530 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9938 Å2 / ksol: 0.368903 e/Å3
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6054 0 57 273 6384
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.522.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 364 5.2 %
Rwork0.254 6602 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ADN.PARAMADN.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://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