[English] 日本語
Yorodumi
- PDB-7vf6: The crystal structure of PurZ0 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vf6
TitleThe crystal structure of PurZ0
ComponentsPurA-like adenylosuccinate synthetase
KeywordsLIGASE / PurA-like adenylosuccinate synthetase
Function / homology
Function and homology information


2-amino-2'-deoxyadenylo-succinate synthase / adenylosuccinate synthase activity / IMP metabolic process / 'de novo' AMP biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
N6-succino-2-amino-2'-deoxyadenylate synthase / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / N6-succino-2-amino-2'-deoxyadenylate synthase
Similarity search - Component
Biological speciesGordonia phage Archimedes (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å
AuthorsTong, Y. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31870049 China
CitationJournal: Nat Microbiol / Year: 2023
Title: Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage.
Authors: Tong, Y. / Wu, X. / Liu, Y. / Chen, H. / Zhou, Y. / Jiang, L. / Li, M. / Zhao, S. / Zhang, Y.
History
DepositionSep 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PurA-like adenylosuccinate synthetase
B: PurA-like adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,52911
Polymers80,9782
Non-polymers1,5519
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-88 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.534, 111.534, 58.277
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein PurA-like adenylosuccinate synthetase


Mass: 40489.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gordonia phage Archimedes (virus) / Gene: 50, SEA_ARCHIMEDES_50 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7L7SI10

-
Non-polymers , 5 types, 596 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 1.26M ammonium sulfate, 0.2M lithium sulfate, 0.1M Tris, pH 8.5, 5mM GTP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 78554 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 12.64 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.068 / Rrim(I) all: 0.159 / Χ2: 0.92 / Net I/σ(I): 6.7 / Num. measured all: 427033
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.735.30.78239400.6980.3780.8690.822100
1.73-1.765.30.66238640.7630.320.7360.854100
1.76-1.795.10.58239290.7910.290.6520.901100
1.79-1.8350.51639000.830.2580.5790.975100
1.83-1.875.50.45138960.8830.2120.4990.975100
1.87-1.915.60.438980.9030.1860.4421.009100
1.91-1.965.60.34139210.9260.1590.3760.981100
1.96-2.025.50.28439180.9430.1330.3140.984100
2.02-2.075.40.24538820.9530.1160.2721.021100
2.07-2.145.20.2139180.960.1020.2341.012100
2.14-2.225.10.19539040.9570.0960.2181.047100
2.22-2.315.70.18539370.9690.0850.2041.126100
2.31-2.415.70.15839270.9730.0730.1741.006100
2.41-2.545.60.14739140.9770.0680.1620.99100
2.54-2.75.50.13339030.980.0620.1480.963100
2.7-2.915.20.11939510.9780.0580.1330.923100
2.91-3.25.80.10839460.9850.0490.1190.842100
3.2-3.665.70.09539630.9870.0440.1050.784100
3.66-4.615.30.08339680.9890.040.0920.647100
4.61-505.50.07840750.9910.0360.0860.55499.9

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phyre2 prediction structure

Resolution: 1.703→37.895 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 1962 2.7 %
Rwork0.1708 70611 -
obs0.1718 72573 92.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.84 Å2 / Biso mean: 15.595 Å2 / Biso min: 3.82 Å2
Refinement stepCycle: final / Resolution: 1.703→37.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 0 124 587 6317
Biso mean--17.93 22.74 -
Num. residues----732
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.703-1.74520.26191030.2148386271
1.7452-1.79240.28381140.2026403874
1.7924-1.84510.24961150.1927421678
1.8451-1.90470.23311360.1898480188
1.9047-1.97270.26361450.1913512094
1.9727-2.05170.2351450.1812527597
2.0517-2.14510.22111480.1664527197
2.1451-2.25820.2611490.1719532998
2.2582-2.39960.21451480.1638536698
2.3996-2.58490.19461480.1688537899
2.5849-2.84490.20441520.1753541499
2.8449-3.25640.19111530.17015445100
3.2564-4.10190.16921520.15195514100
4.1019-37.8950.18181540.1626558299

+
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