[English] 日本語
Yorodumi
- PDB-3ix2: CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM MYCOBAC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ix2
TitleCRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH ACYCLOVIR
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / Mycobacterium tuberculosis / Purine Nucleoside Phosphorylase / Acyclovir
Function / homology
Function and homology information


nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm
Similarity search - Function
Putative purine nucleotide phosphorylase / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
9-HYROXYETHOXYMETHYLGUANINE / PHOSPHATE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis variant bovis AF2122/97 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Authorsde Azevedo Jr., W.F. / Basso, L.A. / Santos, D.S.
CitationJournal: Biochimie / Year: 2012
Title: Crystal structure and molecular dynamics studies of purine nucleoside phosphorylase from Mycobacterium tuberculosis associated with acyclovir.
Authors: Caceres, R.A. / Timmers, L.F. / Ducati, R.G. / da Silva, D.O. / Basso, L.A. / de Azevedo Jr., W.F. / Santos, D.S.
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Source and taxonomy / Category: database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Sep 20, 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: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7599
Polymers82,7983
Non-polymers9616
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-64 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.177, 135.759, 41.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Purine nucleoside phosphorylase / PNP / Pu-NPase / Inosine phosphorylase / Inosine-guanosine phosphorylase


Mass: 27599.457 Da / Num. of mol.: 3 / Fragment: PURINE NUCLEOSIDE PHOSPHORYLASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis variant bovis AF2122/97 (bacteria)
Strain: ATCC BAA-935 / AF2122/97 / Gene: punA, deoD, BQ2027_MB3335 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A539, 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-AC2 / 9-HYROXYETHOXYMETHYLGUANINE


Mass: 225.205 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H11N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 1.79 Å3/Da / Density % sol: 31.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, pH 8.0, 25%PEG 3350, and 25 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR scanner 300 mm plate / Detector: CCD / Date: Feb 2, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2.1→33.94 Å / Num. all: 39559 / Num. obs: 35559 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3 / Num. unique all: 2200 / Rsym value: 0.2 / % possible all: 90

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N3I

1n3i


Resolution: 2.1→33.94 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.876 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.369 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26197 1679 5 %RANDOM
Rwork0.18256 ---
all0.18653 35559 --
obs0.18653 31718 93.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.187 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.03 Å
Refinement stepCycle: LAST / Resolution: 2.1→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5688 0 63 388 6139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0215859
X-RAY DIFFRACTIONr_angle_refined_deg2.3881.9898019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1395783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26722.74219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.37415834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.61551
X-RAY DIFFRACTIONr_chiral_restr0.2920.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024476
X-RAY DIFFRACTIONr_nbd_refined0.2670.23825
X-RAY DIFFRACTIONr_nbtor_refined0.3260.23976
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2629
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3410.2200
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.222
X-RAY DIFFRACTIONr_mcbond_it1.9461.53897
X-RAY DIFFRACTIONr_mcangle_it2.92326198
X-RAY DIFFRACTIONr_scbond_it3.12431962
X-RAY DIFFRACTIONr_scangle_it4.7224.51821
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 125 -
Rwork0.214 2238 -
obs--91.95 %

+
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