[English] 日本語
Yorodumi
- PDB-1dvr: STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dvr
TitleSTRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP
ComponentsADENYLATE KINASE
KeywordsTRANSFERASE (PHOSPHOTRANSFERASE) / NUCLEOSIDE MONOPHOSPHATE KINASE / MYOKINASE
Function / homology
Function and homology information


AMP metabolic process / Interconversion of nucleotide di- and triphosphates / ADP biosynthetic process / adenylate kinase / adenylate kinase activity / nucleotide metabolic process / DNA replication initiation / ATP metabolic process / mitochondrial intermembrane space / phosphorylation ...AMP metabolic process / Interconversion of nucleotide di- and triphosphates / ADP biosynthetic process / adenylate kinase / adenylate kinase activity / nucleotide metabolic process / DNA replication initiation / ATP metabolic process / mitochondrial intermembrane space / phosphorylation / mitochondrion / ATP binding / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase 2 / 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 ...Adenylate kinase 2 / 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
Chem-ATF / Adenylate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.36 Å
AuthorsSchlauderer, G.J. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP.
Authors: Schlauderer, G.J. / Proba, K. / Schulz, G.E.
#1: Journal: Eur.J.Biochem. / Year: 1995
Title: Stability, Activity and Structure of Adenylate Kinase Mutants
Authors: Spuergin, P. / Abele, U. / Schulz, G.E.
#2: Journal: Protein Sci. / Year: 1995
Title: High-Resolution Structures of Adenylate Kinase from Yeast Ligated with Inhibitor Ap5A, Showing the Pathway of Phosphoryl Transfer
Authors: Abele, U. / Schulz, G.E.
#3: 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.
#4: Journal: Nucleic Acids Res. / Year: 1987
Title: The C-DNA Sequence Encoding Cytosolic Adenylate Kinase from Baker'S Yeast (Saccharomyces Cerevisiae)
Authors: Proba, K. / Tomasselli, A.G. / Nielsen, P. / Schulz, G.E.
#5: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of the Complex of Yeast Adenylate Kinase with the Inhibitor Ap5A at 2.6 Angstroms Resolution
Authors: Egner, U. / Tomasselli, A.G. / Schulz, G.E.
#6: Journal: Eur.J.Biochem. / Year: 1986
Title: The Complete Amino Acid Sequence of Adenylate Kinase from Baker'S Yeast
Authors: Tomasselli, A.G. / Mast, E. / Janes, W. / Schiltz, E.
History
DepositionDec 14, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Other
Category: diffrn_source / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET THE HELIX AND SHEET ASSIGNMENTS BELOW ARE AUTOMATIC WITH PROGRAM DSSP.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADENYLATE KINASE
B: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0994
Polymers48,0172
Non-polymers1,0822
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.800, 73.400, 118.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 92 / 2: CIS PROLINE - PRO B 92
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.489945, -0.809503, -0.323511), (-0.812717, 0.289904, 0.505417), (-0.315349, 0.510549, -0.799934)
Vector: 65.3682, 45.295, -12.509)

-
Components

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


Mass: 24008.525 Da / Num. of mol.: 2 / Mutation: D89V, R165I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cellular location: CYTOSOL / Plasmid: PUAKYI / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P07170, adenylate kinase
#2: Chemical ChemComp-ATF / PHOSPHODIFLUOROMETHYLPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 541.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16F2N5O12P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
pH: 6.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.4 mMenzyme1drop
22.5 mMAMPPCF2P1drop
350 mMimidazole1drop
475 mM1dropKCl
50.05 %octyl-beta-glucoside1drop
621 %PEG33501drop
750 mMimidazole1reservoir
828 %PEG33501reservoir

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / 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: 2.36→10 Å / Num. obs: 15793 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.058
Reflection
*PLUS
Rmerge(I) obs: 0.058

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.36→10 Å / σ(F): 0
Details: RESIDUES SER 166 - ASN 169 IN CHAIN HAVE WEAK DENSITY.
RfactorNum. reflection% reflection
Rwork0.191 --
obs0.191 15793 90 %
Displacement parametersBiso mean: 29 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.36→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 66 161 3593
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_it2.41.5
X-RAY DIFFRACTIONx_mcangle_it3.92
X-RAY DIFFRACTIONx_scbond_it6.42
X-RAY DIFFRACTIONx_scangle_it8.72.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
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://pdbjlvh1.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