[English] 日本語
Yorodumi
- PDB-3ees: Structure of the RNA pyrophosphohydrolase BdRppH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ees
TitleStructure of the RNA pyrophosphohydrolase BdRppH
ComponentsProbable pyrophosphohydrolase
KeywordsHYDROLASE / Nudix / RNA pyrophosphohydrolase
Function / homology
Function and homology information


8-oxo-dGTP diphosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA replication / DNA repair / GTP binding / metal ion binding / identical protein binding
Similarity search - Function
Mutator MutT / : / MutY, C-terminal / NUDIX domain / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nudix hydrolase domain profile. ...Mutator MutT / : / MutY, C-terminal / NUDIX domain / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsMessing, S.A. / Gabelli, S.B. / Amzel, L.M.
CitationJournal: Structure / Year: 2009
Title: Structure and Biological Function of the RNA Pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus.
Authors: Messing, S.A. / Gabelli, S.B. / Liu, Q. / Celesnik, H. / Belasco, J.G. / Pineiro, S.A. / Amzel, L.M.
History
DepositionSep 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable pyrophosphohydrolase
B: Probable pyrophosphohydrolase


Theoretical massNumber of molelcules
Total (without water)35,2692
Polymers35,2692
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.491, 70.491, 100.481
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsGel filtration was used to determine the biological assembly.

-
Components

#1: Protein Probable pyrophosphohydrolase


Mass: 17634.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Strain: HD100 / Gene: mutT, Bd0714 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6MPX4, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 4
Details: PEG 4000, Na acetate, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: adsc Q210 / Detector: CCD / Date: Apr 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 6.7 % / Av σ(I) over netI: 63.36 / Number: 152495 / Rmerge(I) obs: 0.054 / Χ2: 1.55 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 22693 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.095096.610.0362.1377
3.254.0999.410.0412.0487.2
2.843.2510010.0651.9387.1
2.582.8499.910.0991.67.2
2.392.5810010.1561.4487.2
2.252.3999.910.2171.357.1
2.142.2510010.3021.2477.1
2.052.1410010.4691.177
1.972.0598.810.6941.146.2
1.91.9792.110.8651.0473.8
ReflectionResolution: 1.9→33.26 Å / Num. obs: 23316 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.043 / Χ2: 1.273 / Net I/σ(I): 63.364
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.9790.3922880.982100
1.97-2.05100.3323000.858100
2.05-2.14100.21423160.954100
2.14-2.259.90.16622841.318100
2.25-2.399.80.12723131.28699.9
2.39-2.589.90.08223091.11999.9
2.58-2.84100.05523451.124100
2.84-3.2510.20.0423441.323100
3.25-4.0910.60.03423761.70499.9
4.09-50100.03324411.93998

-
Phasing

PhasingMethod: MIR
Phasing MIRResolution: 2.7→50 Å / FOM: 0.49 / Reflection: 8125
Phasing MIR der
IDDer set-ID
11
21
31
41
Phasing MIR der site
IDDer-IDBiso (Å)Atom type symbolFract xFract yFract zOccupancy
1141.1236U0.43830.7130.07260.175
1260U0.80390.07690.12170.2666
134.9224U0.28230.93220.03010.0351
2160Hg0.26140.91670.02090.1744
2212.4028Hg0.3360.95270.04370.0516
2360Hg0.80360.41740.10710.0935
2418.1562Hg0.86870.43790.13490.0556
3143.8922Ho0.81570.08360.11890.1036
3239.7193Ho0.42490.70580.06020.0954
3314.5451Ho0.28160.39910.11820.0428
4152.028Sm0.79360.06060.11270.1192
Phasing MIR shell
Resolution (Å)FOMReflection
9.74-500.67396
6.14-9.740.68681
4.8-6.140.57844
4.07-4.80.531027
3.59-4.070.471140
3.25-3.590.471257
2.99-3.250.431349
2.79-2.990.391431

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MIR / Resolution: 1.9→33.26 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.228 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.795 / SU B: 8.251 / SU ML: 0.122 / SU R Cruickshank DPI: 0.178 / SU Rfree: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1188 5.1 %RANDOM
Rwork0.222 ---
obs0.223 23229 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.54 Å2 / Biso mean: 40.295 Å2 / Biso min: 25.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 0 107 2212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222162
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9592918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0265256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53324.135104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79415390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7541512
X-RAY DIFFRACTIONr_chiral_restr0.0910.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021640
X-RAY DIFFRACTIONr_nbd_refined0.190.2846
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21410
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.212
X-RAY DIFFRACTIONr_mcbond_it0.6771.51341
X-RAY DIFFRACTIONr_mcangle_it1.08322043
X-RAY DIFFRACTIONr_scbond_it1.6763978
X-RAY DIFFRACTIONr_scangle_it2.5814.5875
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 96 -
Rwork0.276 1601 -
all-1697 -
obs--100 %

+
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