[English] 日本語
Yorodumi
- PDB-9mgv: Crystal structure of Apo Purine nucleoside phosphorylase from Tri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mgv
TitleCrystal structure of Apo Purine nucleoside phosphorylase from Trichomonas vaginalis (H32 form)
ComponentsPurine nucleoside phosphorylase, putative
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Purine nucleoside phosphorylase / Trichomonas vaginalis
Function / homology
Function and homology information


uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
Purine nucleoside phosphorylase, putative
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Apo Purine nucleoside phosphorylase from Trichomonas vaginalis (H32 form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionDec 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Purine nucleoside phosphorylase, putative


Theoretical massNumber of molelcules
Total (without water)26,6431
Polymers26,6431
Non-polymers00
Water7,080393
1
A: Purine nucleoside phosphorylase, putative
x 6


Theoretical massNumber of molelcules
Total (without water)159,8616
Polymers159,8616
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area19680 Å2
ΔGint-162 kcal/mol
Surface area51070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.073, 93.073, 132.068
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-359-

HOH

21A-396-

HOH

31A-432-

HOH

41A-474-

HOH

51A-574-

HOH

61A-674-

HOH

71A-689-

HOH

-
Components

#1: Protein Purine nucleoside phosphorylase, putative


Mass: 26643.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_454490 / Plasmid: TrvaA.01033.d.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2EU62
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Crystal Screen HT A10: 0.20 M Ammounium Acetate, 0.10 M sodium Acetate, pH 4.6, 30% PEG 4000, TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. plate 14429 well A10 drop 1 , Puck: PSL0905. Cryo: direct

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 24, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.2→46.54 Å / Num. obs: 65118 / % possible obs: 94.9 % / Redundancy: 16.8 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.014 / Rrim(I) all: 0.061 / Χ2: 0.95 / Net I/σ(I): 28.7 / Num. measured all: 1095308
Reflection shellResolution: 1.2→1.22 Å / % possible obs: 60.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.203 / Num. measured all: 10352 / Num. unique obs: 2040 / CC1/2: 0.965 / Rpim(I) all: 0.094 / Rrim(I) all: 0.226 / Χ2: 0.83 / Net I/σ(I) obs: 5.5

-
Processing

Software
NameVersionClassification
PHENIXdev_5508refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→46.54 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1275 3275 5.03 %
Rwork0.1063 --
obs0.1074 65111 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 0 393 2226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072000
X-RAY DIFFRACTIONf_angle_d1.012742
X-RAY DIFFRACTIONf_dihedral_angle_d13.721772
X-RAY DIFFRACTIONf_chiral_restr0.08317
X-RAY DIFFRACTIONf_plane_restr0.009355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.1491870.11671676X-RAY DIFFRACTION60
1.22-1.240.12891130.11031982X-RAY DIFFRACTION71
1.24-1.260.14841100.10852219X-RAY DIFFRACTION79
1.26-1.280.15351250.10592398X-RAY DIFFRACTION86
1.28-1.30.1361260.09982564X-RAY DIFFRACTION91
1.3-1.330.10861360.09982695X-RAY DIFFRACTION95
1.33-1.350.12461560.10252778X-RAY DIFFRACTION99
1.35-1.380.12751650.10392786X-RAY DIFFRACTION100
1.38-1.420.13811710.09922834X-RAY DIFFRACTION100
1.42-1.450.13611570.09362792X-RAY DIFFRACTION100
1.45-1.490.12411330.08942827X-RAY DIFFRACTION100
1.49-1.530.10891430.08882831X-RAY DIFFRACTION100
1.53-1.580.12411500.08862829X-RAY DIFFRACTION100
1.58-1.640.11941200.09342840X-RAY DIFFRACTION100
1.64-1.710.11391650.09832812X-RAY DIFFRACTION100
1.71-1.780.12961420.09622855X-RAY DIFFRACTION100
1.78-1.880.11251550.09842853X-RAY DIFFRACTION100
1.88-20.11141620.10142810X-RAY DIFFRACTION100
2-2.150.13421330.10112868X-RAY DIFFRACTION100
2.15-2.370.11731670.10542834X-RAY DIFFRACTION100
2.37-2.710.11221700.1122849X-RAY DIFFRACTION100
2.71-3.410.14881310.11682917X-RAY DIFFRACTION100
3.41-46.540.14211580.12432987X-RAY DIFFRACTION100

+
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