[English] 日本語
Yorodumi
- PDB-4ake: ADENYLATE KINASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ake
TitleADENYLATE KINASE
ComponentsADENYLATE KINASE
KeywordsPHOSPHOTRANSFERASE / NUCLEOSIDE MONOPHOSPHATE KINASE / ATP:AMP PHOSPHOTRANSFERASE / MYOKINASE
Function / homology
Function and homology information


purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage ...purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity / AMP binding / phosphorylation / magnesium ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSchlauderer, G.J. / Schulz, G.E.
Citation
Journal: Structure / Year: 1996
Title: Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding.
Authors: Muller, C.W. / Schlauderer, G.J. / Reinstein, J. / Schulz, G.E.
#1: Journal: Structure / Year: 1995
Title: Movie of the Structural Changes During a Catalytic Cycle of Nucleoside Monophosphate Kinases
Authors: Vonrhein, C. / Schlauderer, G.J. / Schulz, G.E.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Structure of the Complex between Adenylate Kinase from Escherichia Coli and the Inhibitor Ap5A Refined at 1.9 A Resolution. A Model for a Catalytic Transition State
Authors: Muller, C.W. / Schulz, G.E.
History
DepositionDec 29, 1995Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADENYLATE KINASE
B: ADENYLATE KINASE


Theoretical massNumber of molelcules
Total (without water)47,2402
Polymers47,2402
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.800, 54.500, 71.300
Angle α, β, γ (deg.)67.70, 77.90, 88.40
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999606, -0.012438, 0.025179), (-0.012961, -0.999702, 0.020699), (0.024914, -0.021017, -0.999469)
Vector: 0.8844, 0.9709, 1.3495)

-
Components

#1: Protein ADENYLATE KINASE / / ATP\:AMP PHOSPHOTRANSFERASE / MYOKINASE


Mass: 23620.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOSOL / Plasmid: PAK601 / Production host: Escherichia coli (E. coli) / References: UniProt: P69441, adenylate kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SECONDARY STRUCTURAL ELEMENTS PRESENTED BELOW ARE FROM PROGRAM DSSP. FOR MANUAL ASSIGNMENTS ...THE SECONDARY STRUCTURAL ELEMENTS PRESENTED BELOW ARE FROM PROGRAM DSSP. FOR MANUAL ASSIGNMENTS PLEASE SEE THE PUBLICATION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
250 mMMOPS1droppH6.9
313-18 %PEG60001drop
40.02 %1dropNaN3
523-27 %PEG60001reservoir
650 mMMOPS1reservoirpH6.9

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→10 Å / Num. obs: 17932 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.063
Reflection
*PLUS
Rmerge(I) obs: 0.063

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.183 --
obs0.183 17932 82 %
Displacement parametersBiso mean: 42 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 0 147 3459
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.41.5
X-RAY DIFFRACTIONx_mcangle_it6.42
X-RAY DIFFRACTIONx_scbond_it6.62
X-RAY DIFFRACTIONx_scangle_it9.62.5
Refinement
*PLUS
Rfactor obs: 0.183 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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