[English] 日本語
Yorodumi
- PDB-7dy2: Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dy2
TitleCrystal Structure of Cyanobacterial Circadian Clock Protein KaiC
Components(Circadian clock protein kinase ...) x 2
KeywordsTRANSFERASE / clock protein
Function / homology
Function and homology information


regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / entrainment of circadian clock / protein serine/threonine/tyrosine kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / circadian rhythm / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity ...regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / entrainment of circadian clock / protein serine/threonine/tyrosine kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / circadian rhythm / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / regulation of DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
Circadian clock KaiC, bacteria / : / Circadian clock protein kinase KaiC / : / : / KaiC domain / KaiC domain profile. / KaiC-like domain / KaiC / P-loop containing nucleotide triphosphate hydrolases ...Circadian clock KaiC, bacteria / : / Circadian clock protein kinase KaiC / : / : / KaiC domain / KaiC domain profile. / KaiC-like domain / KaiC / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsFuruike, Y. / Akiyama, S.
CitationJournal: Sci Adv / Year: 2022
Title: Elucidation of master allostery essential for circadian clock oscillation in cyanobacteria.
Authors: Furuike, Y. / Mukaiyama, A. / Ouyang, D. / Ito-Miwa, K. / Simon, D. / Yamashita, E. / Kondo, T. / Akiyama, S.
History
DepositionJan 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Circadian clock protein kinase KaiC
B: Circadian clock protein kinase KaiC
E: Circadian clock protein kinase KaiC
F: Circadian clock protein kinase KaiC
C: Circadian clock protein kinase KaiC
D: Circadian clock protein kinase KaiC
G: Circadian clock protein kinase KaiC
H: Circadian clock protein kinase KaiC
K: Circadian clock protein kinase KaiC
L: Circadian clock protein kinase KaiC
I: Circadian clock protein kinase KaiC
J: Circadian clock protein kinase KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)709,33748
Polymers697,75312
Non-polymers11,58436
Water32418
1
A: Circadian clock protein kinase KaiC
B: Circadian clock protein kinase KaiC
E: Circadian clock protein kinase KaiC
F: Circadian clock protein kinase KaiC
C: Circadian clock protein kinase KaiC
D: Circadian clock protein kinase KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,77325
Polymers348,9176
Non-polymers5,85619
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43280 Å2
ΔGint-210 kcal/mol
Surface area93800 Å2
MethodPISA
2
G: Circadian clock protein kinase KaiC
H: Circadian clock protein kinase KaiC
K: Circadian clock protein kinase KaiC
L: Circadian clock protein kinase KaiC
I: Circadian clock protein kinase KaiC
J: Circadian clock protein kinase KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,56423
Polymers348,8376
Non-polymers5,72817
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41690 Å2
ΔGint-207 kcal/mol
Surface area94480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.803, 206.600, 168.383
Angle α, β, γ (deg.)90.000, 94.690, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Circadian clock protein kinase ... , 2 types, 12 molecules ABEFCDGKLIJH

#1: Protein
Circadian clock protein kinase KaiC


Mass: 58152.750 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria)
Strain: PCC 7942 / FACHB-805 / Gene: kaiC, Synpcc7942_1216, see0011 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q79PF4, non-specific serine/threonine protein kinase
#2: Protein Circadian clock protein kinase KaiC


Mass: 58072.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria)
Strain: PCC 7942 / FACHB-805 / Gene: kaiC, Synpcc7942_1216, see0011 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q79PF4, non-specific serine/threonine protein kinase

-
Non-polymers , 4 types, 54 molecules

#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 313 K / Method: evaporation / pH: 5 / Details: Acetatic acid, Sodium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.038→50 Å / Num. obs: 120308 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 15.6
Reflection shellResolution: 3.038→3.15 Å / Rmerge(I) obs: 0.899 / Num. unique obs: 12016

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GBL

2gbl


Resolution: 3.04→49.24 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.837 / SU B: 78.48 / SU ML: 0.624 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.592 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3256 6048 5 %RANDOM
Rwork0.263 ---
obs0.2662 114215 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 161.94 Å2 / Biso mean: 61.728 Å2 / Biso min: 32 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0 Å20.21 Å2
2---3.22 Å2-0 Å2
3---4.51 Å2
Refinement stepCycle: final / Resolution: 3.04→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38547 0 712 18 39277
Biso mean--69.09 48.64 -
Num. residues----5548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01339914
X-RAY DIFFRACTIONr_bond_other_d0.0020.01832625
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.64254430
X-RAY DIFFRACTIONr_angle_other_deg1.1931.57974751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.31255497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90121.5051747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.087155015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.28315247
X-RAY DIFFRACTIONr_chiral_restr0.030.25830
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0247159
X-RAY DIFFRACTIONr_gen_planes_other0.0020.028842
LS refinement shellResolution: 3.04→3.117 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.416 357 -
Rwork0.374 7466 -
obs--87.27 %
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)
10.62760.39090.30551.41750.47430.4404-0.0357-0.1670.0456-0.10610.007-0.03260.00410.11470.02870.22780.0482-0.24590.2668-0.00950.307220.56-12.32991.993
20.78060.5196-0.00461.02990.20190.3447-0.0452-0.3327-0.06840.00240.0003-0.08530.01430.04410.0450.25570.071-0.25210.348-0.01390.2796-2.542-12.55109.845
30.1394-0.15360.07011.27860.43140.27-0.02720.02720.0708-0.1137-0.0228-0.0267-0.06930.00330.05010.312-0.0141-0.30560.16640.00810.3212-7.7419.64255.597
40.35040.07670.121.56870.33020.17640.03130.0030.0438-0.0773-0.0097-0.1349-0.01840.1177-0.02160.1924-0.0253-0.20580.2434-0.0140.283217.773-1.38264.507
50.34040.26580.11490.88320.32820.44510.0185-0.13680.0006-0.0161-0.02390.0174-0.0282-0.04340.00540.19490.0406-0.23310.3132-0.05330.2836-28.492-2.322100.445
60.16980.06170.1791.15610.44770.63180.0263-0.00350.0141-0.0232-0.0601-0.0587-0.0516-0.12220.03380.24020.044-0.28360.1928-0.04970.3625-30.6379.00673.288
70.29380.093-0.24410.61850.29070.4728-0.10890.27330.20930.02310.16440.11540.0486-0.1858-0.05550.2899-0.0403-0.3290.29120.14050.420812.36-24.651155.791
80.7420.57360.28541.11490.4040.3121-0.0089-0.0072-0.00090.01630.01390.0903-0.0422-0.1168-0.0050.19730.0062-0.22220.24950.04380.31699.282-38.001181.05
90.38130.3301-0.07551.39240.1580.3561-0.08450.32420.0111-0.0059-0.0015-0.10840.00640.01270.0860.1924-0.0461-0.20010.43070.02580.250360.423-37.544153.91
100.6461-0.00350.00451.62270.94240.8584-0.1550.51810.21440.06030.07230.15470.06710.06080.08270.2998-0.1347-0.26450.47530.19470.27137.535-24.694141.309
110.74790.63430.28351.58470.39650.1978-0.0031-0.0864-0.10280.1062-0.00780.003-0.029-0.03380.01090.28-0.001-0.23650.18780.01540.247532.678-50.925193.429
120.5060.51990.0951.2530.34320.2598-0.04930.0502-0.1005-0.0120.0127-0.0554-0.02050.05680.03660.241-0.0115-0.25850.2428-0.02170.337758.168-50.997179.556
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 498
2X-RAY DIFFRACTION1A602 - 603
3X-RAY DIFFRACTION2B18 - 496
4X-RAY DIFFRACTION2B703
5X-RAY DIFFRACTION3E18 - 497
6X-RAY DIFFRACTION3E604
7X-RAY DIFFRACTION4F17 - 497
8X-RAY DIFFRACTION4F602 - 603
9X-RAY DIFFRACTION5C19 - 498
10X-RAY DIFFRACTION5C602 - 603
11X-RAY DIFFRACTION6D18 - 496
12X-RAY DIFFRACTION6D602 - 603
13X-RAY DIFFRACTION7G18 - 497
14X-RAY DIFFRACTION7G602 - 603
15X-RAY DIFFRACTION8H18 - 499
16X-RAY DIFFRACTION8H602 - 603
17X-RAY DIFFRACTION9K15 - 497
18X-RAY DIFFRACTION9K602 - 603
19X-RAY DIFFRACTION10L18 - 497
20X-RAY DIFFRACTION10L602 - 603
21X-RAY DIFFRACTION11I18 - 498
22X-RAY DIFFRACTION11I602
23X-RAY DIFFRACTION12J17 - 497
24X-RAY DIFFRACTION12J703

+
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