[English] 日本語
Yorodumi
- PDB-5xzw: Crystal structure of Rad53 1-466 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xzw
TitleCrystal structure of Rad53 1-466
ComponentsSerine/threonine-protein kinase RAD53
KeywordsTRANSFERASE / serine/threonine-protein kinase / FHA domain / checkpoint kinase
Function / homology
Function and homology information


deoxyribonucleoside triphosphate biosynthetic process / G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / meiotic recombination checkpoint signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / negative regulation of phosphorylation / dual-specificity kinase / DNA replication origin binding / negative regulation of DNA damage checkpoint ...deoxyribonucleoside triphosphate biosynthetic process / G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / meiotic recombination checkpoint signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / negative regulation of phosphorylation / dual-specificity kinase / DNA replication origin binding / negative regulation of DNA damage checkpoint / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / protein localization / protein tyrosine kinase activity / protein kinase activity / phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase Rad53 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Serine/threonine-protein kinase Rad53 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase RAD53
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWeng, J.H. / Tsai, M.D.
Funding support Taiwan, 4items
OrganizationGrant numberCountry
National Health Research InstituteNHRI-EX100-10002NI Taiwan
Academia SinicaAS-104-TP-B05 Taiwan
Ministry of Science and TechnologyMOST105-0210-01-12-01 Taiwan
Ministry of Science and TechnologyMOST106-0210-01-15-04 Taiwan
Citation
Journal: Biochemistry / Year: 2017
Title: Phospho-Priming Confers Functionally Relevant Specificities for Rad53 Kinase Autophosphorylation
Authors: Chen, E.S. / Weng, J.H. / Chen, Y.H. / Wang, S.C. / Liu, X.X. / Huang, W.C. / Matsui, T. / Kawano, Y. / Liao, J.H. / Lim, L.H. / Bessho, Y. / Huang, K.F. / Wu, W.J. / Tsai, M.D.
#1: Journal: To Be Published
Title: Phospho-priming Confers Functionally Relevant Specificities for Rad53 Kinase Autophosphorylation
Authors: Weng, J.H. / Tsai, M.D.
History
DepositionJul 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase RAD53
B: Serine/threonine-protein kinase RAD53


Theoretical massNumber of molelcules
Total (without water)105,0132
Polymers105,0132
Non-polymers00
Water88349
1
A: Serine/threonine-protein kinase RAD53


Theoretical massNumber of molelcules
Total (without water)52,5061
Polymers52,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase RAD53


Theoretical massNumber of molelcules
Total (without water)52,5061
Polymers52,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-12 kcal/mol
Surface area36680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.809, 115.809, 141.269
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Serine/threonine-protein kinase RAD53 / CHEK2 homolog / Serine-protein kinase 1


Mass: 52506.469 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RAD53, MEC2, SAD1, SPK1, YPL153C, P2588 / Production host: Escherichia coli (E. coli) / References: UniProt: P22216, dual-specificity kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 100MM CACODYLATE, 0.4M NACL, 1.5M (NH4)2SO4 / PH range: 6.5

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL15A110.9
SYNCHROTRONSPring-8 BL44XU20.9
Detector
TypeIDDetectorDate
RAYONIX MX300HE1CCDMar 27, 2014
RAYONIX MX300HE2CCDApr 17, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.91
ReflectionResolution: 2.8→30 Å / Num. obs: 27160 / % possible obs: 98.6 % / Redundancy: 9 % / Biso Wilson estimate: 48.14 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.699 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.528 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2843 1994 7.92 %
Rwork0.2672 --
obs0.2686 25178 91.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→29.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5599 0 0 49 5648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085677
X-RAY DIFFRACTIONf_angle_d1.3967677
X-RAY DIFFRACTIONf_dihedral_angle_d17.7062007
X-RAY DIFFRACTIONf_chiral_restr0.07912
X-RAY DIFFRACTIONf_plane_restr0.006981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7997-2.86970.3246740.3247879X-RAY DIFFRACTION50
2.8697-2.94720.3377970.33371134X-RAY DIFFRACTION63
2.9472-3.03380.31591390.32441568X-RAY DIFFRACTION88
3.0338-3.13170.33171550.31741760X-RAY DIFFRACTION99
3.1317-3.24350.35561540.32651777X-RAY DIFFRACTION100
3.2435-3.37310.32421560.31241790X-RAY DIFFRACTION100
3.3731-3.52640.2711570.27541792X-RAY DIFFRACTION100
3.5264-3.7120.26171540.26721799X-RAY DIFFRACTION100
3.712-3.94410.28441540.24781791X-RAY DIFFRACTION100
3.9441-4.24780.27111540.23251813X-RAY DIFFRACTION100
4.2478-4.67370.22781510.21321824X-RAY DIFFRACTION100
4.6737-5.34660.24931530.24081821X-RAY DIFFRACTION100
5.3466-6.7230.30591630.27471846X-RAY DIFFRACTION100
6.723-29.53010.28831330.26951590X-RAY DIFFRACTION82
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)
12.66131.7264-2.54861.8372-1.66933.7338-0.30430.05410.17340.42960.1280.0359-0.24060.01970.11510.8207-0.2644-0.06020.22530.00370.394-51.788123.96120.4872
22.852-2.1078-0.0433.38090.36553.4298-0.10370.06080.14410.01690.0491-1.3230.04281.35270.04790.7172-0.48180.00750.91730.09970.9294-22.083520.91735.6799
33.32381.0812-0.69381.95070.35712.03460.0623-0.123-0.04590.096-0.20670.22210.1999-0.23830.10270.6917-0.7071-0.06941.0991-0.06310.4142-36.370839.346643.9048
41.19661.0225-0.20641.7539-0.55481.42870.094-0.32370.01180.2067-0.0389-0.0038-0.06470.0945-0.02880.5295-0.66180.15850.5959-0.08710.3976-28.526455.06658.0259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 258 )
2X-RAY DIFFRACTION2chain 'A' and (resid 259 through 465 )
3X-RAY DIFFRACTION3chain 'B' and (resid 32 through 221 )
4X-RAY DIFFRACTION4chain 'B' and (resid 222 through 467 )

+
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