[English] 日本語
Yorodumi
- PDB-9fxe: D204N mutant of Purine Nucleoside Phosphorylase from E.coli in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fxe
TitleD204N mutant of Purine Nucleoside Phosphorylase from E.coli in complex with N2,3-etheno-2-aminopurine
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / fluorescent ligand
Function / homology
Function and homology information


purine nucleoside interconversion / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / DNA damage response / identical protein binding / membrane / 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
: / PHOSPHATE ION / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsNarczyk, M. / Stachelska-Wierzchowska, A. / Wierzchowski, J.
Funding support Poland, 2items
OrganizationGrant numberCountry
Ministry of Science and Higher Education (Poland)661-79/2024 Poland
Ministry of Science and Higher Education (Poland)17.610.011-110 Poland
CitationJournal: Int J Mol Sci / Year: 2024
Title: Interaction of Tri-Cyclic Nucleobase Analogs with Enzymes of Purine Metabolism: Xanthine Oxidase and Purine Nucleoside Phosphorylase.
Authors: Stachelska-Wierzchowska, A. / Narczyk, M. / Wierzchowski, J. / Bzowska, A. / Wielgus-Kutrowska, B.
History
DepositionJul 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7059
Polymers77,9433
Non-polymers7626
Water3,153175
1
A: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
hetero molecules

A: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,41018
Polymers155,8866
Non-polymers1,52512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area22660 Å2
ΔGint-170 kcal/mol
Surface area44460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.525, 120.525, 241.206
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11B-425-

HOH

-
Components

#1: Protein Purine nucleoside phosphorylase DeoD-type / PNP


Mass: 25980.961 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: deoD, pup, b4384, JW4347 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABP8, purine-nucleoside phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-A1IEC / N,2,3-etheno-2-aminopurine / 1~{H}-imidazo[2,1-b]purine


Mass: 159.148 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H5N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: Citrate buffer pH 5.2, amonium sulphate 24% w/v

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.12→48.22 Å / Num. obs: 59360 / % possible obs: 97.46 % / Redundancy: 40.3 % / Biso Wilson estimate: 38.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.0455 / Rrim(I) all: 0.299 / Net I/σ(I): 15.24
Reflection shellResolution: 2.12→2.196 Å / Redundancy: 34.5 % / Rmerge(I) obs: 3.43 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 5825 / CC1/2: 0.589 / Rpim(I) all: 0.587 / Rrim(I) all: 3.481 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→48.22 Å / SU ML: 0.2545 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.393
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2331 2794 4.83 %
Rwork0.2044 55112 -
obs0.2058 57906 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.45 Å2
Refinement stepCycle: LAST / Resolution: 2.12→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5388 0 51 175 5614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675527
X-RAY DIFFRACTIONf_angle_d0.8357452
X-RAY DIFFRACTIONf_chiral_restr0.0543842
X-RAY DIFFRACTIONf_plane_restr0.0076959
X-RAY DIFFRACTIONf_dihedral_angle_d14.67981995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.160.36951380.3052778X-RAY DIFFRACTION100
2.16-2.20.33961440.3032760X-RAY DIFFRACTION100
2.2-2.240.35461330.31762479X-RAY DIFFRACTION90.01
2.24-2.280.3975840.42051759X-RAY DIFFRACTION62.84
2.28-2.330.27081500.2482740X-RAY DIFFRACTION100
2.33-2.390.27961280.23562805X-RAY DIFFRACTION100
2.39-2.450.28241340.23022785X-RAY DIFFRACTION100
2.45-2.510.24741630.21762798X-RAY DIFFRACTION100
2.51-2.590.24311330.21262773X-RAY DIFFRACTION100
2.59-2.670.21161540.19272793X-RAY DIFFRACTION100
2.67-2.770.27591460.20472787X-RAY DIFFRACTION99.97
2.77-2.880.2531190.2082851X-RAY DIFFRACTION99.97
2.88-3.010.241350.20182809X-RAY DIFFRACTION100
3.01-3.170.26831630.19642816X-RAY DIFFRACTION100
3.17-3.360.20321530.18972818X-RAY DIFFRACTION99.97
3.36-3.620.19971270.19412854X-RAY DIFFRACTION100
3.62-3.990.26211490.21262759X-RAY DIFFRACTION96.8
3.99-4.570.17671380.15692898X-RAY DIFFRACTION99.93
4.57-5.750.17931390.17922937X-RAY DIFFRACTION99.97
5.75-48.220.22311640.19953113X-RAY DIFFRACTION99.79

+
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