[English] 日本語
Yorodumi
- PDB-4i5t: Crystal structure of yeast Ap4A phosphorylase Apa2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i5t
TitleCrystal structure of yeast Ap4A phosphorylase Apa2
Components5',5'''-P-1,P-4-tetraphosphate phosphorylase 2
KeywordsTRANSFERASE / Ap4A phosphorylase / Ap4A
Function / homology
Function and homology information


sulfate adenylyltransferase (ADP) / sulfate adenylyltransferase (ADP) activity / ATP adenylyltransferase / bis(5'-nucleosyl)-tetraphosphatase activity / ATP:ADP adenylyltransferase activity / nucleotide biosynthetic process / nucleoside catabolic process / ATP binding / nucleus / cytoplasm
Similarity search - Function
ATP adenylyltransferase / Ap4A phosphorylase 1/2 / ATP adenylyltransferase, C-terminal / Ap4A phosphorylase 1/2-like / Ap4A phosphorylase 1/2, N-terminal domain / : / ATP adenylyltransferase C-terminal domain / Ap4A phosphorylase N-terminal domain / HIT family, subunit A / HIT-like superfamily ...ATP adenylyltransferase / Ap4A phosphorylase 1/2 / ATP adenylyltransferase, C-terminal / Ap4A phosphorylase 1/2-like / Ap4A phosphorylase 1/2, N-terminal domain / : / ATP adenylyltransferase C-terminal domain / Ap4A phosphorylase N-terminal domain / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsJiang, Y.L. / Hou, W.T. / Chen, Y. / Zhou, C.Z.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structures of yeast Apa2 reveal catalytic insights into a canonical AP4A phosphorylase of the histidine triad superfamily
Authors: Hou, W.T. / Li, W.Z. / Chen, Y. / Jiang, Y.L. / Zhou, C.Z.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2
B: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2


Theoretical massNumber of molelcules
Total (without water)75,8062
Polymers75,8062
Non-polymers00
Water4,035224
1
A: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2


Theoretical massNumber of molelcules
Total (without water)37,9031
Polymers37,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2


Theoretical massNumber of molelcules
Total (without water)37,9031
Polymers37,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2

B: 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2


Theoretical massNumber of molelcules
Total (without water)75,8062
Polymers75,8062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area2030 Å2
ΔGint-8 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.760, 74.460, 112.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2 / ATP adenylyltransferase / Ap4A phosphorylase II / AP / A phosphorylase / Diadenosine 5' / 5'''-P1 / ...ATP adenylyltransferase / Ap4A phosphorylase II / AP / A phosphorylase / Diadenosine 5' / 5'''-P1 / P4-tetraphosphate phosphorylase / AP-4-A phosphorylase


Mass: 37902.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: APA2, YDR530C, D9719.33 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22108, ATP adenylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.03 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG 2K, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.3→47.49 Å / Num. obs: 27391 / % possible obs: 97.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.5

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→44.844 Å / SU ML: 0.74 / σ(F): 1.35 / Phase error: 29.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2777 1374 5.03 %
Rwork0.2029 --
obs0.2067 27333 97.02 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.629 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4013 Å2-0 Å20 Å2
2---4.5689 Å20 Å2
3---1.1676 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 0 224 5094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084989
X-RAY DIFFRACTIONf_angle_d1.2516771
X-RAY DIFFRACTIONf_dihedral_angle_d15.2041861
X-RAY DIFFRACTIONf_chiral_restr0.085755
X-RAY DIFFRACTIONf_plane_restr0.005878
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.38220.37511080.2646219183
2.3822-2.47760.35641380.2638238791
2.4776-2.59040.3511270.2547260699
2.5904-2.72690.28391510.23432629100
2.7269-2.89770.34071390.22662652100
2.8977-3.12140.32191150.20942683100
3.1214-3.43540.28031720.20132623100
3.4354-3.93230.26911530.19672676100
3.9323-4.95330.22051420.15962713100
4.9533-44.85290.24741290.1973279998

+
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