[English] 日本語
Yorodumi
- PDB-6pc1: Crystal structure of Helicobacter pylori PPX/GppA (E143A) in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pc1
TitleCrystal structure of Helicobacter pylori PPX/GppA (E143A) in complex with ppGpp
ComponentsGuanosine pentaphosphate phosphohydrolase
KeywordsHYDROLASE / pppGpp / ppGpp / PPX / GppA / Polyphosphate
Function / homology
Function and homology information


pyrophosphatase activity / metal ion binding
Similarity search - Function
Pyrophosphatase, GppA/Ppx-type / : / Ppx/GppA phosphatase, domain III / : / Ppx/GppA phosphatase / Ppx/GppA phosphatase family / ATPase, nucleotide binding domain
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / (2S)-2-hydroxybutanedioic acid / PHOSPHATE ION / Guanosine pentaphosphate phosphohydrolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsSong, H. / Wang, C. / Shaw, G.X. / Ji, X.
CitationJournal: Febs J. / Year: 2020
Title: Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori.
Authors: Song, H. / Dharmasena, M.N. / Wang, C. / Shaw, G.X. / Cherry, S. / Tropea, J.E. / Jin, D.J. / Ji, X.
History
DepositionJun 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Guanosine pentaphosphate phosphohydrolase
B: Guanosine pentaphosphate phosphohydrolase
C: Guanosine pentaphosphate phosphohydrolase
D: Guanosine pentaphosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,14523
Polymers222,3904
Non-polymers3,75519
Water6,648369
1
A: Guanosine pentaphosphate phosphohydrolase
B: Guanosine pentaphosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,14212
Polymers111,1952
Non-polymers1,94710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-49 kcal/mol
Surface area38950 Å2
MethodPISA
2
C: Guanosine pentaphosphate phosphohydrolase
D: Guanosine pentaphosphate phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,00311
Polymers111,1952
Non-polymers1,8089
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-58 kcal/mol
Surface area38410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.507, 194.507, 136.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Guanosine pentaphosphate phosphohydrolase


Mass: 55597.512 Da / Num. of mol.: 4 / Mutation: E143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: HPG27_257 / Production host: Escherichia coli (E. coli) / References: UniProt: B5ZA44

-
Non-polymers , 6 types, 388 molecules

#2: Chemical
ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O5
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (v/v) PEG3350, 0.2 M Ammonium tartrate, 15 mM Malic acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 6, 2014
RadiationMonochromator: Mirror1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→40 Å / Num. obs: 63095 / % possible obs: 99.3 % / Redundancy: 4.2 % / Rpim(I) all: 0.085 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5219 / % possible all: 74.6

-
Processing

Software
NameVersionClassification
PHENIX(dev_3352: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hi0

3hi0


Resolution: 2.76→40 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.71
RfactorNum. reflection% reflection
Rfree0.2222 1000 1.59 %
Rwork0.1783 --
obs0.1791 63041 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.76→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15102 0 225 369 15696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01715602
X-RAY DIFFRACTIONf_angle_d0.58621006
X-RAY DIFFRACTIONf_dihedral_angle_d12.3485836
X-RAY DIFFRACTIONf_chiral_restr0.1142432
X-RAY DIFFRACTIONf_plane_restr0.0032563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7598-2.90530.38861140.28257226X-RAY DIFFRACTION78
2.9053-3.08720.25251500.24459096X-RAY DIFFRACTION99
3.0872-3.32550.27851470.23319130X-RAY DIFFRACTION100
3.3255-3.660.23581460.18489185X-RAY DIFFRACTION100
3.66-4.18910.21321470.15489110X-RAY DIFFRACTION99
4.1891-5.2760.17971470.13899158X-RAY DIFFRACTION99
5.276-40.40570.19271490.16469136X-RAY DIFFRACTION98

+
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