[English] 日本語
Yorodumi
- PDB-7apu: Structure of Adenylate kinase from Escherichia coli in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7apu
TitleStructure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution.
ComponentsAdenylate kinase
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / ADENYLATE KINASE / COMPLEX WITH TWO ADP / PROTEIN DYNAMICS
Function / homology
Function and homology information


purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / phosphorylation ...purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
AuthorsGrundstom, C. / Wolf-Watz, M. / Nam, K. / Sauer, U.H.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Biochemistry / Year: 2021
Title: Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions.
Authors: Ojeda-May, P. / Mushtaq, A.U. / Rogne, P. / Verma, A. / Ovchinnikov, V. / Grundstrom, C. / Dulko-Smith, B. / Sauer, U.H. / Wolf-Watz, M. / Nam, K.
History
DepositionOct 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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)48,9958
Polymers47,2402
Non-polymers1,7556
Water10,611589
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4974
Polymers23,6201
Non-polymers8773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4974
Polymers23,6201
Non-polymers8773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.754, 82.226, 78.783
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Components on special symmetry positions
IDModelComponents
11B-408-

HOH

-
Components

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


Mass: 23620.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: adk, dnaW, plsA, b0474, JW0463 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P69441, adenylate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50 % / Description: rods
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: AdK at 18.3 mg/ml was mixed with 5 mM each of AMP and GTP in 30 mM MOPS buffer pH 7, containing 50 mM NaCl. Hanging drop: 2 ul of AdK, preincubated with AMP and GTP, and 2 ul of precipitant ...Details: AdK at 18.3 mg/ml was mixed with 5 mM each of AMP and GTP in 30 mM MOPS buffer pH 7, containing 50 mM NaCl. Hanging drop: 2 ul of AdK, preincubated with AMP and GTP, and 2 ul of precipitant buffer containing 30% PEG 4000, 0.2 M NH4CH3CO2 (Ammonium Acetate), buffered with 100 mM CH3COONa (Sodium Acetate) adjusted to pH 4.6.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97498 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97498 Å / Relative weight: 1
ReflectionResolution: 1.36→44.81 Å / Num. obs: 99761 / % possible obs: 98.1 % / Redundancy: 7.3 % / Biso Wilson estimate: 16.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.025 / Rrim(I) all: 0.067 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.36-1.417.31.0171.995060.6820.3971.09496
5.27-44.816.80.03219220.9980.0130.03598.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimless0.5.15data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AKE

1ake


Resolution: 1.36→44.81 Å / SU ML: 0.163 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.8338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206 5028 5.04 %
Rwork0.1843 94693 -
obs0.1854 99721 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.65 Å2
Refinement stepCycle: LAST / Resolution: 1.36→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 110 589 4011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01373559
X-RAY DIFFRACTIONf_angle_d1.56414834
X-RAY DIFFRACTIONf_chiral_restr0.1007537
X-RAY DIFFRACTIONf_plane_restr0.0119623
X-RAY DIFFRACTIONf_dihedral_angle_d18.8035531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.34861690.31182995X-RAY DIFFRACTION93.97
1.38-1.390.30721410.30033114X-RAY DIFFRACTION96.79
1.39-1.410.31561710.28093074X-RAY DIFFRACTION96.52
1.41-1.430.311590.26723062X-RAY DIFFRACTION96.24
1.43-1.450.27911710.25973093X-RAY DIFFRACTION97.37
1.45-1.460.23751550.25093079X-RAY DIFFRACTION96.25
1.47-1.490.27691780.23193108X-RAY DIFFRACTION96.93
1.49-1.510.23721530.22663092X-RAY DIFFRACTION97.42
1.51-1.530.23361660.21743103X-RAY DIFFRACTION97.15
1.53-1.560.24441700.21863107X-RAY DIFFRACTION97.36
1.56-1.580.25261570.2143134X-RAY DIFFRACTION97.34
1.58-1.610.2451740.21793113X-RAY DIFFRACTION97.74
1.61-1.640.23091610.20963146X-RAY DIFFRACTION97.87
1.64-1.680.21680.20813139X-RAY DIFFRACTION97.81
1.68-1.710.25461530.20293135X-RAY DIFFRACTION97.11
1.71-1.750.20891680.19223116X-RAY DIFFRACTION97.45
1.75-1.80.2321660.19023130X-RAY DIFFRACTION97.51
1.8-1.850.22021660.19123129X-RAY DIFFRACTION97.98
1.85-1.90.23541690.19093176X-RAY DIFFRACTION98.44
1.9-1.960.23991820.18973167X-RAY DIFFRACTION98.3
1.96-2.030.19191750.18853161X-RAY DIFFRACTION98.87
2.03-2.110.21861900.1953193X-RAY DIFFRACTION99.12
2.11-2.210.20971580.17843161X-RAY DIFFRACTION97.85
2.21-2.330.19491720.17243223X-RAY DIFFRACTION99.39
2.33-2.470.21651630.18053229X-RAY DIFFRACTION99.21
2.47-2.660.23471720.18483239X-RAY DIFFRACTION99.48
2.66-2.930.20021670.18713275X-RAY DIFFRACTION99.42
2.93-3.350.18511800.17373234X-RAY DIFFRACTION98.78
3.35-4.220.16981610.15563334X-RAY DIFFRACTION99.69
4.22-44.810.16051930.1513432X-RAY DIFFRACTION98.94

+
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