[English] 日本語
Yorodumi
- PDB-8bqf: Adenylate Kinase L107I MUTANT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bqf
TitleAdenylate Kinase L107I MUTANT
ComponentsAdenylate kinase
KeywordsTRANSFERASE / COMPLEX
Function / homology
Function and homology information


purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / CDP biosynthetic process / nucleoside diphosphate metabolic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage ...purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / CDP biosynthetic process / nucleoside diphosphate metabolic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity / AMP binding / phosphorylation / magnesium ion binding / ATP binding / cytoplasm / cytosol
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
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsScheerer, D. / Adkar, B.V. / Bhattacharyya, S. / Levy, D. / Iljina, M. / Iljina, I. / Dym, O. / Haran, G. / Shakhnovich, E.I.
Funding supportEuropean Union, Israel, 2items
OrganizationGrant numberCountry
European Research Council (ERC)742637European Union
Israel Science Foundation1250/19 Israel
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase.
Authors: Scheerer, D. / Adkar, B.V. / Bhattacharyya, S. / Levy, D. / Iljina, M. / Riven, I. / Dym, O. / Haran, G. / Shakhnovich, E.I.
History
DepositionNov 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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
C: Adenylate kinase
D: Adenylate kinase
E: Adenylate kinase
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,24712
Polymers154,7486
Non-polymers5,4986
Water4,017223
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7082
Polymers25,7911
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7082
Polymers25,7911
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7082
Polymers25,7911
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7082
Polymers25,7911
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7082
Polymers25,7911
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7082
Polymers25,7911
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.975, 84.490, 218.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

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


Mass: 25791.402 Da / Num. of mol.: 6 / Mutation: L107I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: adk, dnaW, plsA, b0474, JW0463 / Production host: Escherichia coli (E. coli) / References: UniProt: P69441, adenylate kinase
#2: Chemical
ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H29N10O22P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 7.5% PEG 3,350, 7.5% PEG 4,000, 7.5% PEG 2,000, 7.5% PEG 5,000 monomethyl ether, 0.07M ammonium nitrate, 2.5% ethylene glycol and 0.05M MES pH=7.
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.3405 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Mar 20, 2022
RadiationMonochromator: Ga / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3405 Å / Relative weight: 1
ReflectionResolution: 2.05→21.04 Å / Num. obs: 93318 / % possible obs: 99.69 % / Redundancy: 8.1 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1043 / Rpim(I) all: 0.03909 / Rrim(I) all: 0.1117 / Net I/σ(I): 20.47
Reflection shellResolution: 2.05→2.123 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.4044 / Mean I/σ(I) obs: 4.39 / Num. unique obs: 8992 / CC1/2: 0.931 / CC star: 0.982 / Rpim(I) all: 0.1585 / Rrim(I) all: 0.435 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F7U

7f7u
PDB Unreleased entry


Resolution: 2.05→21.04 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.648 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25789 4792 4.9 %RANDOM
Rwork0.21882 ---
obs0.22073 93318 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.461 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--1.35 Å2-0 Å2
3----1.45 Å2
Refinement stepCycle: 1 / Resolution: 2.05→21.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9486 0 338 223 10047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310044
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159444
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.66113718
X-RAY DIFFRACTIONr_angle_other_deg1.3091.58521718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04451264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.00622.444450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.319151638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.311563
X-RAY DIFFRACTIONr_chiral_restr0.0910.21392
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211171
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022023
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3612.8835078
X-RAY DIFFRACTIONr_mcbond_other2.362.8825076
X-RAY DIFFRACTIONr_mcangle_it3.5114.3056334
X-RAY DIFFRACTIONr_mcangle_other3.514.3056334
X-RAY DIFFRACTIONr_scbond_it2.6883.0464965
X-RAY DIFFRACTIONr_scbond_other2.6873.0464965
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1474.4527385
X-RAY DIFFRACTIONr_long_range_B_refined5.58633.84410662
X-RAY DIFFRACTIONr_long_range_B_other5.58833.84810627
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.052 Å
RfactorNum. reflection% reflection
Rfree0.328 342 -
Rwork0.271 6856 -
obs--100 %

+
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