[English] 日本語
Yorodumi
- PDB-2q07: Crystal structure of AF0587, a protein of unknown function -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q07
TitleCrystal structure of AF0587, a protein of unknown function
ComponentsUncharacterized protein AF0587
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / 10391c / protein AF0587 / monomer / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


pentosyltransferase activity / tRNA modification / RNA binding
Similarity search - Function
Domain of unknown function (DUF5591) / Uracil-DNA glycosylase-like / Domain of unknown function DUF5591 / TGT, patch-forming C2 domain superfamily / ArcTGT, C2 domain / PUA domain / PUA domain / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. ...Domain of unknown function (DUF5591) / Uracil-DNA glycosylase-like / Domain of unknown function DUF5591 / TGT, patch-forming C2 domain superfamily / ArcTGT, C2 domain / PUA domain / PUA domain / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Uracil-DNA glycosylase-like domain superfamily / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase / PUA-like superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PUA domain-containing protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsSugadev, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of AF0587, a protein of unknown function.
Authors: Sugadev, R. / Burley, S.K. / Swaminathan, S.
History
DepositionMay 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein AF0587


Theoretical massNumber of molelcules
Total (without water)35,2781
Polymers35,2781
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.791, 58.745, 51.258
Angle α, β, γ (deg.)90.00, 96.91, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Uncharacterized protein AF0587


Mass: 35277.723 Da / Num. of mol.: 1 / Fragment: Residues 233-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Species: Archaeoglobus fulgidus / Strain: VC-16, DSM 4304, JCM 9628, NBRC 100126 / Gene: AF_0587 / Plasmid: pSGX3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29668
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.94 Å3/Da / Density % sol: 36.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Magnesium formate, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2007 / Details: Mirrors
RadiationMonochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 16046 / Num. obs: 16046 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15
Reflection shellResolution: 2.04→2.13 Å / Redundancy: 1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1 / % possible all: 52

-
Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.04→32.04 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 95114.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 757 4.9 %RANDOM
Rwork0.245 ---
obs0.245 15539 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.3266 Å2 / ksol: 0.379082 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å2-0.15 Å2
2--1.75 Å20 Å2
3----2.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.04→32.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 0 84 2266
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.661.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it2.62
X-RAY DIFFRACTIONc_scangle_it3.762.5
LS refinement shellResolution: 2.04→2.13 Å / Rfactor Rfree error: 0.057 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 38 3.8 %
Rwork0.371 969 -
obs--33.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.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