[English] 日本語
Yorodumi
- PDB-5zoc: Crystal structure of APRT from Y. pseudotuberculosis with bound a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zoc
TitleCrystal structure of APRT from Y. pseudotuberculosis with bound adenine (C2 space group).
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / adenine phosphoribosyltransferase / Yersinia pseudotuberculosis / adenine
Function / homology
Function and homology information


adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / cytosol
Similarity search - Function
: / Adenine phosphoribosyl transferase / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesYersinia pseudotuberculosis IP 32953 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsPavithra, G.C. / Ramagopal, U.A.
CitationJournal: To be published
Title: Crystal structure of APRT from Y. pseudotuberculosis with bound adenine (C2 space group).
Authors: Pavithra, G.C. / Ramagopal, U.A.
History
DepositionApr 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3243
Polymers20,1661
Non-polymers1582
Water79344
1
A: Adenine phosphoribosyltransferase
hetero molecules

A: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6486
Polymers40,3322
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3700 Å2
ΔGint-30 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.714, 77.873, 54.074
Angle α, β, γ (deg.)90.000, 112.610, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-332-

HOH

-
Components

#1: Protein Adenine phosphoribosyltransferase / APRT


Mass: 20165.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis IP 32953 (bacteria)
Strain: IP32953 / Gene: apt, YPTB0991 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q66DQ2, adenine phosphoribosyltransferase
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.83 Å3/Da / Density % sol: 56.53 % / Mosaicity: 0.673 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG3350, 0.1M Tris-Hcl pH 8.5, 0.2M Sodium Acetate with 5mM adenine and 5% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 15046 / % possible obs: 95.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.017 / Rrim(I) all: 0.039 / Χ2: 0.875 / Net I/σ(I): 42.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.013.40.1495120.9920.0850.1730.79763.9
2.01-2.053.80.1455910.9910.0780.1650.79876.7
2.05-2.094.30.1166650.9940.0590.1310.80186.3
2.09-2.1350.1157850.9950.0550.1270.91198.7
2.13-2.185.30.1097710.9950.0510.1210.944100
2.18-2.235.30.0967820.9950.0450.1070.965100
2.23-2.295.30.0867780.9970.040.0950.966100
2.29-2.355.40.0717890.9970.0330.0780.976100
2.35-2.425.40.0667710.9970.0310.0730.999100
2.42-2.495.40.0567730.9980.0260.0620.996100
2.49-2.585.40.0477900.9980.0210.0510.953100
2.58-2.695.30.0437860.9980.020.0470.938100
2.69-2.815.40.047640.9990.0180.0440.928100
2.81-2.965.30.0357860.9980.0160.0390.87199.7
2.96-3.145.30.0317890.9990.0140.0340.77899.6
3.14-3.395.20.0317860.9980.0150.0340.76299.4
3.39-3.7350.0337820.9960.0160.0360.76699.1
3.73-4.264.80.0337720.9950.0170.0380.74898.6
4.26-5.374.60.0337790.9950.0180.0380.73897.4
5.371-504.70.037950.9970.0150.0340.66598.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MB6

4mb6


Resolution: 1.98→49.92 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.046 / SU ML: 0.108 / SU R Cruickshank DPI: 0.1693 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.151
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 704 4.8 %RANDOM
Rwork0.1984 ---
obs0.1999 13968 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.05 Å2 / Biso mean: 31.64 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-0 Å2-0.37 Å2
2--0.25 Å2-0 Å2
3---1.59 Å2
Refinement stepCycle: final / Resolution: 1.98→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 11 44 1398
Biso mean--34.92 29.37 -
Num. residues----177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191408
X-RAY DIFFRACTIONr_bond_other_d00.021332
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.9971920
X-RAY DIFFRACTIONr_angle_other_deg0.59133092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8845184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33124.28656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36215234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.84157
X-RAY DIFFRACTIONr_chiral_restr0.0650.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211579
X-RAY DIFFRACTIONr_gen_planes_other00.02275
LS refinement shellResolution: 1.981→2.032 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 32 -
Rwork0.261 553 -
all-585 -
obs--49.79 %
Refinement TLS params.Method: refined / Origin x: 21.307 Å / Origin y: -0.884 Å / Origin z: 7.837 Å
111213212223313233
T0.1959 Å20.0036 Å20.0585 Å2-0.0686 Å20.0017 Å2--0.0329 Å2
L2.2728 °20.0389 °2-1.4398 °2-1.1449 °2-0.479 °2--4.316 °2
S0.1992 Å °0.0081 Å °0.1274 Å °0.2443 Å °-0.0031 Å °0.1559 Å °-0.1431 Å °-0.3924 Å °-0.1961 Å °

+
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