[English] 日本語
Yorodumi
- PDB-2q16: Structure of the E. coli inosine triphosphate pyrophosphatase Rgd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q16
TitleStructure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP
ComponentsHAM1 protein homolog
KeywordsHYDROLASE / ITP pyrophosphatase x-ray structure enzyme mechanism substrate
Function / homology
Function and homology information


XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / ribonucleoside triphosphate phosphatase activity / magnesium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
dITP/XTP pyrophosphatase / Maf protein - #10 / Ham1-like protein / Ham1 family / Maf protein / Inosine triphosphate pyrophosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
INOSINE 5'-TRIPHOSPHATE / dITP/XTP pyrophosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsSinger, A.U. / Lam, R. / Proudfoot, M. / Skarina, T. / Savchenko, A. / Yakunin, A.F.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli.
Authors: Savchenko, A. / Proudfoot, M. / Skarina, T. / Singer, A. / Litvinova, O. / Sanishvili, R. / Brown, G. / Chirgadze, N. / Yakunin, A.F.
History
DepositionMay 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details
Remark 999sequence These residues belong to a TEV cleavage site.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HAM1 protein homolog
B: HAM1 protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,25912
Polymers46,9522
Non-polymers1,30810
Water7,386410
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.646, 120.646, 66.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein HAM1 protein homolog


Mass: 23475.980 Da / Num. of mol.: 2 / Mutation: D69A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yggV / Plasmid: pET15-b-based p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RP
References: UniProt: P52061, nucleoside-triphosphate diphosphatase

-
Non-polymers , 5 types, 420 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ITT / INOSINE 5'-TRIPHOSPHATE / INOSINE TRIPHOSPHATE


Mass: 508.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N4O14P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG 4K, 200 mM Ammonium Sulfate, 100 mM Sodium Acetate, 2% iso-Propanol, 20 mM Calcium Chloride, 10mM ITP, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2006 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.95→500 Å / Num. all: 36421 / Num. obs: 36385 / % possible obs: 99.96 % / Redundancy: 19.4 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 39.9
Reflection shellResolution: 1.95→2 Å / Redundancy: 17.7 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2359 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→26.98 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.965 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20829 1813 5 %RANDOM
Rwork0.17086 ---
all0.17278 36421 --
obs0.17278 34514 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.725 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→26.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 0 74 410 3406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223058
X-RAY DIFFRACTIONr_angle_refined_deg1.6782.0024168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6015392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99824.16125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26315491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.061520
X-RAY DIFFRACTIONr_chiral_restr0.1230.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022290
X-RAY DIFFRACTIONr_nbd_refined0.2170.21487
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22089
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2310
X-RAY DIFFRACTIONr_metal_ion_refined0.1910.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.230
X-RAY DIFFRACTIONr_mcbond_it0.8331.51938
X-RAY DIFFRACTIONr_mcangle_it1.50223095
X-RAY DIFFRACTIONr_scbond_it2.51831145
X-RAY DIFFRACTIONr_scangle_it4.0874.51072
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 121 -
Rwork0.176 2510 -
obs-2631 99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0008-0.07620.57682.06080.32531.80790.0415-0.00430.0196-0.0823-0.0664-0.09230.0573-0.08730.0248-0.15050.00460.011-0.09080.0249-0.105833.77587.591411.8241
21.7-0.271-1.30691.64760.65992.0238-0.03850.0003-0.13360.0461-0.02290.02920.0786-0.05890.0613-0.07480.04420.0017-0.11410.02-0.119133.84418.557242.9215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 19721 - 217
2X-RAY DIFFRACTION2BB3 - 19523 - 215

+
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