[English] 日本語
Yorodumi
- PDB-4ntz: Crystal structure of Adenylate kinase from Streptococcus pneumoniae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ntz
TitleCrystal structure of Adenylate kinase from Streptococcus pneumoniae
ComponentsAdenylate kinase
KeywordsTRANSFERASE / adenylate kinase / capsular polysaccharide / growth / CORE / NMP/LID domain / AMP/ATP binding / phosphotransferase
Function / homology
Function and homology information


adenylate kinase / AMP kinase activity / AMP salvage / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsThach, T.T. / Luong, T.T. / Lee, S.H. / Rhee, D.K.
CitationJournal: FEBS Open Bio / Year: 2014
Title: Adenylate kinase from Streptococcus pneumoniae is essential for growth through its catalytic activity
Authors: Thach, T.T. / Luong, T.T. / Lee, S.H. / Rhee, D.K.
History
DepositionDec 3, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2512
Polymers24,1551
Non-polymers961
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.220, 53.700, 50.870
Angle α, β, γ (deg.)90.000, 114.460, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Adenylate kinase / AK / ATP-AMP transphosphorylase / ATP-AMP phosphotransferase / Adenylate monophosphate kinase


Mass: 24155.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: D39 / Gene: adk, SPD_0214 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04ML5, adenylate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 2.0M (NH4)2SO4, 0.1M CHES pH 9.5, 0.2M Li2SO4, 0.1M CsCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→25.05 Å / Num. all: 23924 / Num. obs: 23924 / % possible obs: 97.84 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 6.8 / % possible all: 98.72

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
PHENIX1.7.2_869refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→25.046 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.46 / σ(F): 1.41 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1223 5.12 %RANDOM
Rwork0.1838 ---
obs0.1857 23897 97.73 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.853 Å2 / ksol: 0.411 e/Å3
Displacement parametersBiso max: 44.22 Å2 / Biso mean: 14.4084 Å2 / Biso min: 4.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.6837 Å2-0 Å2-2.6537 Å2
2---2.6173 Å2-0 Å2
3----0.0664 Å2
Refinement stepCycle: LAST / Resolution: 1.69→25.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 5 356 2035
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d1.39
X-RAY DIFFRACTIONf_bond_d0.019
LS refinement shellResolution: 1.69→1.73 Å / % reflection obs: 98.72 %

+
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