[English] 日本語
Yorodumi
- PDB-7syc: Crystal Structure of Nucleoside triphosphate pyrophosphohydrolase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7syc
TitleCrystal Structure of Nucleoside triphosphate pyrophosphohydrolase from Klebsiella pneumoniae subsp. pneumoniae
Components7,8-dihydro-8-oxoguanine-triphosphatase
KeywordsHYDROLASE / SSGCID / DNA repair / nudix hydrolase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / metal ion binding
Similarity search - Function
Mutator MutT / : / MutY, C-terminal / NUDIX domain / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of Nucleoside triphosphate pyrophosphohydrolase from Klebsiella pneumoniae subsp. pneumoniae
Authors: DeBouver, N.D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 7,8-dihydro-8-oxoguanine-triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9292
Polymers15,9051
Non-polymers241
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.140, 67.140, 136.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

21A-389-

HOH

-
Components

#1: Protein 7,8-dihydro-8-oxoguanine-triphosphatase / 8-oxo-dGTP diphosphatase / 8-oxo-dGTP diphosphatase MutT


Mass: 15905.060 Da / Num. of mol.: 1 / Fragment: KlpnC.00264.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: mutT, E3U38_03970, NCTC9504_05440, RJA_22585 / Plasmid: KlpnC.00264.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Y0Q4X2, 8-oxo-dGTP diphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: KlpnC.00264.a.B1.PW38992 [Barcode: 322156a9] [pin_id: llw0-5] [collection: aps21idf 9/23/2021] [crystallization conditions: MCSG1 A9 0.1M HEPES/NaOH, pH 7.5, 0.2M MgCl2, 25% (w/v) PEG 3350] [cryo: 10% EG]

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 21, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→44.19 Å / Num. obs: 12903 / % possible obs: 99.9 % / Redundancy: 13.577 % / Biso Wilson estimate: 39.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.046 / Χ2: 0.935 / Net I/σ(I): 32.73 / Num. measured all: 175186
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.0514.3460.5765.06132419239230.9480.598100
2.05-2.1114.0980.3767.68128869149140.9750.39100
2.11-2.1714.2540.3228.99125018778770.9820.334100
2.17-2.2414.2030.26510.78122578638630.9870.275100
2.24-2.3114.2420.21913.05116648198190.9930.227100
2.31-2.3914.10.17715.88113658068060.9950.183100
2.39-2.4814.0910.14419.47111047887880.9960.149100
2.48-2.5814.0330.11423.46105537527520.9980.118100
2.58-2.713.8410.08430.44100217247240.9990.088100
2.7-2.8313.6530.06638.0294076896890.9990.069100
2.83-2.9813.3390.05743.3488846666660.9990.06100
2.98-3.1613.2020.04850.2483836356350.9990.05100
3.16-3.3812.8110.0456.3276745995990.9990.042100
3.38-3.6512.8050.03862.7471585595590.9990.039100
3.65-412.7210.03166.38665352352310.032100
4-4.4712.6540.02971.26617548848810.031100
4.47-5.1612.6640.02772.12535742342310.028100
5.16-6.3212.290.02770.17453536936910.028100
6.32-8.9411.8750.02469.9236223063050.9990.02699.7
8.94-44.199.6460.02566.0917461911810.9990.02694.8

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20rc3_4406refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A6S

3a6s


Resolution: 2→44.19 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 1300 10.08 %
Rwork0.1979 11603 -
obs0.2024 12903 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.79 Å2 / Biso mean: 47.9441 Å2 / Biso min: 22.71 Å2
Refinement stepCycle: final / Resolution: 2→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 1 110 1077
Biso mean--55.03 50.63 -
Num. residues----122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.080.26431350.254112601395100
2.08-2.170.28691430.216812461389100
2.18-2.290.24821240.219612651389100
2.29-2.430.27841330.225112761409100
2.43-2.620.27661320.249212791411100
2.62-2.880.26281490.221212631412100
2.88-3.30.25531500.21212971447100
3.3-4.160.22671600.171213141474100
4.16-44.190.22011740.17991403157799
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)
15.00552.7614-1.43845.0288-1.07832.58230.1071-0.2091-0.1444-0.010.22080.50240.4751-0.0946-0.22190.2912-0.018-0.08820.41580.15350.4096-29.692319.49082.5525
26.88312.6095-0.2962.77441.32823.5294-0.27511.57860.4369-0.8160.9135-0.414-0.37850.218-0.19840.26360.08080.040.58540.21080.3858-15.361736.0321-8.8077
36.16232.59-0.82948.3879-0.70958.013-0.09081.4974-1.4744-1.33690.02640.57810.6066-0.4863-0.15530.39210.0946-0.07510.9697-0.04240.4521-22.713926.2895-10.1932
47.42511.6888-4.16836.78133.07599.95810.08050.51-0.76891.0540.06-0.3942.1537-0.07020.4290.39510.0036-0.09020.33250.01750.522-21.23517.79716.5986
55.23571.2878-5.40894.3380.44226.4242-0.10910.1828-0.41180.02240.0403-1.18780.44290.375-0.11980.22970.0355-0.04370.45340.0570.5576-14.539422.65280.8175
60.85490.82660.59834.54611.32633.25330.4214-0.1820.63270.0548-0.11520.3014-0.2718-0.1091-0.21580.20230.04780.0030.45620.07120.3296-24.438229.99643.4429
74.48795.0626-0.2324.6850.45571.34660.0291-0.1884-0.3659-0.2294-0.1811-0.13140.2742-0.04430.11660.20010.0292-0.00880.41630.10420.3954-30.223824.1081.6513
88.04340.10282.36686.6989-1.79294.96370.18321.5505-0.9822-0.9727-0.2339-0.48640.58970.2445-0.01620.33970.03790.0890.7591-0.11610.4637-10.492126.6089-7.4831
99.1745-3.49363.62797.0247-1.32725.889-0.35072.94810.1884-0.9483-0.00540.8923-0.1157-1.05160.4860.3050.1115-0.03431.00320.30260.4192-18.3135.7261-13.6626
107.3272-0.19151.54552.6932-1.90588.5508-0.0861.49120.8611-0.4114-0.04560.4257-1.096-2.10210.08810.33340.1118-0.04960.960.12820.5716-28.934634.7503-8.2291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 11 )A-1 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 21 )A12 - 21
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 36 )A22 - 36
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 45 )A37 - 45
5X-RAY DIFFRACTION5chain 'A' and (resid 46 through 60 )A46 - 60
6X-RAY DIFFRACTION6chain 'A' and (resid 61 through 74 )A61 - 74
7X-RAY DIFFRACTION7chain 'A' and (resid 75 through 87 )A75 - 87
8X-RAY DIFFRACTION8chain 'A' and (resid 88 through 101 )A88 - 101
9X-RAY DIFFRACTION9chain 'A' and (resid 102 through 109 )A102 - 109
10X-RAY DIFFRACTION10chain 'A' and (resid 110 through 129 )A110 - 129

+
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