[English] 日本語
Yorodumi
- PDB-5u7f: Co-bound dihydroneopterin triphosphate pyrophosphohydrolase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u7f
TitleCo-bound dihydroneopterin triphosphate pyrophosphohydrolase from E. coli
ComponentsDihydroneopterin triphosphate diphosphatase
KeywordsHYDROLASE / Nudix hydrolase / Dihydroneopterin Triphosphate Pyrophosphohydrolase / Metal ion binding / Tetranuclear
Function / homology
Function and homology information


dihydroneopterin triphosphate diphosphatase / dihydroneopterin triphosphate pyrophosphohydrolase activity / AMP biosynthetic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / dATP diphosphatase activity / ATP biosynthetic process / folic acid biosynthetic process / metal ion binding
Similarity search - Function
Dihydroneopterin triphosphate diphosphatase / : / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Dihydroneopterin triphosphate diphosphatase / : / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Dihydroneopterin triphosphate diphosphatase
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.789 Å
AuthorsNguyen, E. / Hill, S.E. / Lieberman, R.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Kimberly Clark United States
National Science Foundation (NSF, United States)0845445 United States
CitationJournal: PLoS ONE / Year: 2017
Title: Metal ion coordination in the E. coli Nudix hydrolase dihydroneopterin triphosphate pyrophosphatase: New clues into catalytic mechanism.
Authors: Hill, S.E. / Nguyen, E. / Ukachukwu, C.U. / Freeman, D.M. / Quirk, S. / Lieberman, R.L.
History
DepositionDec 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Mar 16, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydroneopterin triphosphate diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7567
Polymers17,3281
Non-polymers4286
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dihydroneopterin triphosphate diphosphatase
hetero molecules

A: Dihydroneopterin triphosphate diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,51114
Polymers34,6552
Non-polymers85612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2780 Å2
ΔGint-179 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.600, 43.090, 57.230
Angle α, β, γ (deg.)90.00, 91.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-329-

HOH

31A-356-

HOH

41A-420-

HOH

-
Components

#1: Protein Dihydroneopterin triphosphate diphosphatase / Dihydroneopterin triphosphate pyrophosphatase / dATP pyrophosphohydrolase


Mass: 17327.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: nudB, Z2917, ECs2575 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AFC1, dihydroneopterin triphosphate diphosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Crystals were grown in 36% PEG 8000, 0.05M Ammonium Sulfate. Crystals were soaked in 0.5mM dihydroneopterin and 5mM CoCl2.

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.606 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.606 Å / Relative weight: 1
ReflectionResolution: 1.789→57.199 Å / Num. obs: 23041 / % possible obs: 94.84 % / Redundancy: 6.9 % / Net I/σ(I): 12.61

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata scaling
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 201C

201c


Resolution: 1.789→57.199 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 27.65
RfactorNum. reflection% reflection
Rfree0.2402 2328 10.1 %
Rwork0.1771 --
obs0.1835 23041 93.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.789→57.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 14 134 1323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191234
X-RAY DIFFRACTIONf_angle_d1.2581648
X-RAY DIFFRACTIONf_dihedral_angle_d13.819440
X-RAY DIFFRACTIONf_chiral_restr0.055185
X-RAY DIFFRACTIONf_plane_restr0.007210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7887-1.82520.4687680.4256580X-RAY DIFFRACTION44
1.8252-1.86490.40751270.27841129X-RAY DIFFRACTION90
1.8649-1.90830.30131260.24881243X-RAY DIFFRACTION95
1.9083-1.9560.30851320.20871266X-RAY DIFFRACTION95
1.956-2.00890.24671530.19381229X-RAY DIFFRACTION95
2.0089-2.0680.26561410.19071279X-RAY DIFFRACTION96
2.068-2.13480.23061290.21227X-RAY DIFFRACTION97
2.1348-2.21110.27171370.18891255X-RAY DIFFRACTION96
2.2111-2.29960.29571460.1851280X-RAY DIFFRACTION97
2.2996-2.40430.26441550.19051246X-RAY DIFFRACTION97
2.4043-2.53110.2671510.19591265X-RAY DIFFRACTION98
2.5311-2.68960.25861330.17091311X-RAY DIFFRACTION98
2.6896-2.89730.29751480.19291267X-RAY DIFFRACTION98
2.8973-3.18880.23651460.1711267X-RAY DIFFRACTION99
3.1888-3.65020.23921410.15731277X-RAY DIFFRACTION99
3.6502-4.59860.1851430.14311295X-RAY DIFFRACTION99
4.5986-57.22870.18561520.15711297X-RAY DIFFRACTION99

+
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