[English] 日本語
Yorodumi
- PDB-6eas: Co-crystal of pseudokinase DRIK1 (drought responsive inactive kin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6eas
TitleCo-crystal of pseudokinase DRIK1 (drought responsive inactive kinase 1) bound to ENMD-2076
Componentsdrought responsive inactive kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Receptor-like kinase / pseudokinase / maize / ENMD-2076 / Structural Genomics Consortium / TRANSFERASE-TRANSFERASE INHIBITOR complex / SGC
Function / homology
Function and homology information


protein kinase activity / ATP binding / membrane
Similarity search - Function
Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-J3A / Protein kinase domain-containing protein / Protein kinase superfamily protein
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAquino, B. / Counago, R.M. / Fala, A.M. / Massirer, K.B. / Elkins, J.M. / Arruda, P. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: To be Published
Title: Co-crystal of pseudokinase DRIK1 with ENMD-2076
Authors: Aquino, B. / Counago, R.M. / Fala, A.M. / Massirer, K.B. / Elkins, J.M. / Arruda, P.
History
DepositionAug 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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: drought responsive inactive kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2533
Polymers34,7861
Non-polymers4682
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint1 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.506, 61.790, 65.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein drought responsive inactive kinase 1 / DRIK1


Mass: 34785.602 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 183-488)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Plasmid: pNIC28a-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4F901, UniProt: C0P4K9*PLUS
#2: Chemical ChemComp-J3A / 6-(4-methylpiperazin-1-yl)-N-(5-methyl-1H-pyrazol-3-yl)-2-[(E)-2-phenylethenyl]pyrimidin-4-amine


Mass: 375.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25N7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.76 Å3/Da / Density % sol: 30.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1 mM zinc chloride, 22% PEG6000, 100 mM MES, pH 6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2→28.91 Å / Num. obs: 17144 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) all: 0.06 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2 / Num. measured obs: 8360 / Num. unique obs: 1238 / CC1/2: 0.723 / Rpim(I) all: 0.537 / Rrim(I) all: 1.025 / Χ2: 1 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CPY

6cpy


Resolution: 2→28.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.343 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.182 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25136 753 4.4 %RANDOM
Rwork0.20741 ---
obs0.20947 16362 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0 Å2
2---0.5 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 2→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1987 0 34 52 2073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0142062
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171814
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.6582799
X-RAY DIFFRACTIONr_angle_other_deg0.8881.6344204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7695260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87321.15895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80715319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.711514
X-RAY DIFFRACTIONr_chiral_restr0.0550.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02396
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_it3.0724.7191049
X-RAY DIFFRACTIONr_mcbond_other3.0724.7181048
X-RAY DIFFRACTIONr_mcangle_it4.2667.0661306
X-RAY DIFFRACTIONr_mcangle_other4.2657.0671307
X-RAY DIFFRACTIONr_scbond_it3.4284.981013
X-RAY DIFFRACTIONr_scbond_other3.4274.981013
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9937.3631494
X-RAY DIFFRACTIONr_long_range_B_refined6.85157.0332360
X-RAY DIFFRACTIONr_long_range_B_other6.85257.0362361
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 57 -
Rwork0.288 1176 -
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://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