[English] 日本語
Yorodumi
- PDB-6t1b: Crystal structure of YlmD from Geobacillus stearothermophilus in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t1b
TitleCrystal structure of YlmD from Geobacillus stearothermophilus in complex with inosine
ComponentsYlmD
KeywordsHYDROLASE / Purine metabolism / enzyme / deaminase / phosphorylase / nucleoside salvage / zinc-binding protein
Function / homology
Function and homology information


adenosine deaminase / 2'-deoxyadenosine deaminase activity / S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / adenosine deaminase activity / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / copper ion binding
Similarity search - Function
CNF1/YfiH-like putative cysteine hydrolases / CNF1/YfiH-like putative cysteine hydrolases / Multi-copper polyphenol oxidoreductase / Multi-copper polyphenol oxidoreductase superfamily / Multi-copper polyphenol oxidoreductase laccase / Cytotoxic necrotizing factor-like, catalytic / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSINE / Purine nucleoside phosphorylase YlmD
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsReikine, S. / Modis, Y.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Wellcome Trust101908/Z/13/Z United Kingdom
Wellcome Trust217191/Z/19/Z United Kingdom
Wellcome Trust106260/Z/14/Z United Kingdom
European Research Council (ERC)HORIZON2020/ERC 648889 United Kingdom
European Research Council (ERC)FP7/2007-2013 260961 United Kingdom
CitationJournal: Cell / Year: 2020
Title: FAMIN Is a Multifunctional Purine Enzyme Enabling the Purine Nucleotide Cycle.
Authors: Cader, M.Z. / de Almeida Rodrigues, R.P. / West, J.A. / Sewell, G.W. / Md-Ibrahim, M.N. / Reikine, S. / Sirago, G. / Unger, L.W. / Iglesias-Romero, A.B. / Ramshorn, K. / Haag, L.M. / ...Authors: Cader, M.Z. / de Almeida Rodrigues, R.P. / West, J.A. / Sewell, G.W. / Md-Ibrahim, M.N. / Reikine, S. / Sirago, G. / Unger, L.W. / Iglesias-Romero, A.B. / Ramshorn, K. / Haag, L.M. / Saveljeva, S. / Ebel, J.F. / Rosenstiel, P. / Kaneider, N.C. / Lee, J.C. / Lawley, T.D. / Bradley, A. / Dougan, G. / Modis, Y. / Griffin, J.L. / Kaser, A.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YlmD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3344
Polymers29,9351
Non-polymers3993
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-37 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.556, 48.483, 134.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein YlmD


Mass: 29934.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P84138
#2: Chemical ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 6000, 0.5 M NaCl, 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 9, 2018 / Details: Horizontal and vertical mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→45.62 Å / Num. obs: 85886 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.053 / Net I/σ(I): 12.4
Reflection shellResolution: 1.2→1.243 Å / Redundancy: 6.3 % / Rmerge(I) obs: 3.571 / Num. unique all: 8462 / Num. unique obs: 12741 / CC1/2: 0.377 / Rpim(I) all: 1.521 / Rrim(I) all: 3.889 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDS11data reduction
PHASER1.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T8H

1t8h


Resolution: 1.2→45.615 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1669 4212 4.95 %
Rwork0.1528 56728 -
obs0.1535 85564 69.4 %
all-8239 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.22 Å2 / Biso mean: 23.9947 Å2 / Biso min: 8.58 Å2
Refinement stepCycle: final / Resolution: 1.2→45.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 33 208 2312
Biso mean--35.16 32.85 -
Num. residues----271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.21970.2594270.274853614
1.2197-1.24070.2562340.266562316
1.2407-1.26330.2298330.249270918
1.2633-1.28760.2004430.243280921
1.2876-1.31390.2194570.225998826
1.3139-1.34240.2595660.2374126033
1.3424-1.37370.1892810.23149339
1.3737-1.4080.2374910.2253180547
1.408-1.44610.25391340.2169218557
1.4461-1.48860.23841620.2214311880
1.4886-1.53670.24582140.2151380999
1.5367-1.59160.20021840.19523878100
1.5916-1.65530.17432180.1733844100
1.6553-1.73070.17922150.16233901100
1.7307-1.82190.15772070.15633876100
1.8219-1.93610.15612000.14013896100
1.9361-2.08560.14251840.12913942100
2.0856-2.29540.13371960.13483936100
2.2954-2.62760.15432000.13953942100
2.6276-3.31030.14551880.14174015100
3.3103-45.610.17062230.14394163100

+
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