[English] 日本語
Yorodumi
- PDB-5x6l: Crystal structure of Notothenia coriiceps adenylate kinase variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x6l
TitleCrystal structure of Notothenia coriiceps adenylate kinase variant
Componentsadenylate kinase
KeywordsTRANSFERASE / phosphorylation
Function / homology
Function and homology information


nucleoside triphosphate adenylate kinase activity / (d)CMP kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / adenylate kinase activity / nucleoside-diphosphate kinase / nucleoside diphosphate kinase activity / ATP metabolic process ...nucleoside triphosphate adenylate kinase activity / (d)CMP kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / adenylate kinase activity / nucleoside-diphosphate kinase / nucleoside diphosphate kinase activity / ATP metabolic process / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase isoenzyme 1 / Adenylate kinase, isozyme 1/5 / 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
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase isoenzyme 1
Similarity search - Component
Biological speciesNotothenia coriiceps (black rockcod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.862 Å
AuthorsBae, E. / Moon, S. / Kim, J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Rural Development AdministrationPJ01111201 Korea, Republic Of
National Research Foundation of KoreaNRF-2016R1D1A1A09916821 Korea, Republic Of
CitationJournal: To Be Published
Title: TBD
Authors: Bae, E. / Moon, S. / Kim, J.
History
DepositionFeb 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)44,9475
Polymers43,0182
Non-polymers1,9293
Water1,964109
1
A: adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5213
Polymers21,5091
Non-polymers1,0122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-4 kcal/mol
Surface area9080 Å2
MethodPISA
2
B: adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4252
Polymers21,5091
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-3 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.444, 105.444, 83.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein adenylate kinase


Mass: 21508.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Notothenia coriiceps (black rockcod) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R2JFU6*PLUS
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS XP_010788477.1 FOR THIS SAMPLE SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2M lithium sulfate, 0.1M acetate pH4.0, 45% PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 40301 / % possible obs: 100 % / Redundancy: 6.5 % / Net I/σ(I): 21.34
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.621 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X6K

5x6k


Resolution: 1.862→47.156 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2063 2013 5.03 %RANDOM
Rwork0.1788 ---
obs0.1802 40055 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.862→47.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 0 119 109 3100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073036
X-RAY DIFFRACTIONf_angle_d1.184100
X-RAY DIFFRACTIONf_dihedral_angle_d14.4351200
X-RAY DIFFRACTIONf_chiral_restr0.041454
X-RAY DIFFRACTIONf_plane_restr0.005504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8619-1.90850.25851270.21282682X-RAY DIFFRACTION100
1.9085-1.96010.22131610.19922655X-RAY DIFFRACTION100
1.9601-2.01780.25411190.17722695X-RAY DIFFRACTION100
2.0178-2.08290.21511530.17672664X-RAY DIFFRACTION100
2.0829-2.15740.22091380.1742689X-RAY DIFFRACTION100
2.1574-2.24370.17851300.16782707X-RAY DIFFRACTION100
2.2437-2.34580.19641470.16742674X-RAY DIFFRACTION100
2.3458-2.46950.21241460.1722698X-RAY DIFFRACTION100
2.4695-2.62420.20951390.1762700X-RAY DIFFRACTION100
2.6242-2.82680.19451310.17912723X-RAY DIFFRACTION100
2.8268-3.11130.22731610.19512728X-RAY DIFFRACTION100
3.1113-3.56130.20351520.1842737X-RAY DIFFRACTION100
3.5613-4.48630.19121590.16712768X-RAY DIFFRACTION100
4.4863-47.17110.20541500.18232922X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1767-0.6616-0.350.7296-0.01260.47150.10540.02240.0171-0.085-0.08810.0057-0.02990.0204-00.16740.00560.01060.19230.00830.167622.661942.2187-21.5665
21.6061-0.0525-0.12130.8823-0.17680.54860.05230.0403-0.0903-0.0283-0.0144-0.02070.041-0.04550.03750.1236-0.0011-0.00050.16870.02650.135-0.920828.6465-1.1862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 193 )
2X-RAY DIFFRACTION2chain 'B' and (resid 8 through 193 )

+
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