[English] 日本語
Yorodumi
- PDB-3aap: Crystal Structure of Lp1NTPDase from Legionella pneumophila -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3aap
TitleCrystal Structure of Lp1NTPDase from Legionella pneumophila
ComponentsEctonucleoside triphosphate diphosphohydrolase I
KeywordsHYDROLASE / Adenosine Triphosphatase / NTPDase
Function / homology
Function and homology information


hydrolase activity / nucleotide binding / metal ion binding
Similarity search - Function
Exopolyphosphatase. Domain 2 / Nucleoside phosphatase GDA1/CD39 / GDA1/CD39 (nucleoside phosphatase) family / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ectonucleoside triphosphate diphosphohydrolase I
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVivian, J.P. / Beddoe, T. / Rossjohn, J.
CitationJournal: Structure / Year: 2010
Title: Crystal Structure of a Legionella pneumophila Ecto -Triphosphate Diphosphohydrolase, A Structural and Functional Homolog of the Eukaryotic NTPDases
Authors: Vivian, J.P. / Riedmaier, P. / Ge, H. / Le Nours, J. / Sansom, F.M. / Wilce, M.C.J. / Byres, E. / Dias, M. / Schmidberger, J.W. / Cowan, P.J. / d'Apice, A.J.F. / Hartland, E.L. / Rossjohn, J. / Beddoe, T.
History
DepositionNov 24, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ectonucleoside triphosphate diphosphohydrolase I


Theoretical massNumber of molelcules
Total (without water)40,0331
Polymers40,0331
Non-polymers00
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.779, 103.779, 75.419
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-444-

HOH

-
Components

#1: Protein Ectonucleoside triphosphate diphosphohydrolase I


Mass: 40032.625 Da / Num. of mol.: 1 / Fragment: UNP residues 41-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / Gene: lpg1905 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5ZUA2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO AUTHOR, RESIDUE 149VAL IS A NATURAL VARIANT OF UNIPROT/TREMBL Q5ZUA2, AND WILL BE ...ACCORDING TO AUTHOR, RESIDUE 149VAL IS A NATURAL VARIANT OF UNIPROT/TREMBL Q5ZUA2, AND WILL BE REPORTED TO UNIPROT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20-24%(w/v) PEG 3350, 0.2M Na Formate, 0.1M Bis-Tris propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 62027 / % possible obs: 99.9 % / Redundancy: 21.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 33.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 20.7 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 4.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CJ1

3cj1


Resolution: 1.6→37.72 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.376 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20668 3142 5.1 %RANDOM
Rwork0.18834 ---
obs0.1893 58843 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.226 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 0 423 3215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222866
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9353913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3415352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.36225.903144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22415445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.538154
X-RAY DIFFRACTIONr_chiral_restr0.0990.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022244
X-RAY DIFFRACTIONr_nbd_refined0.2230.21453
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2350
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.236
X-RAY DIFFRACTIONr_mcbond_it1.2171.51799
X-RAY DIFFRACTIONr_mcangle_it1.90122837
X-RAY DIFFRACTIONr_scbond_it2.88331233
X-RAY DIFFRACTIONr_scangle_it4.2744.51076
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 237 -
Rwork0.234 4295 -
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