[English] 日本語
Yorodumi
- PDB-4zmf: Phosphorylated Aspartate in the Crystal Structure of the Alpha-ki... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zmf
TitlePhosphorylated Aspartate in the Crystal Structure of the Alpha-kinase domain of Myosin-II Heavy Chain Kinase A
ComponentsMyosin heavy chain kinase A
KeywordsTRANSFERASE / Aspartyl phosphate intermediate
Function / homology
Function and homology information


myosin-heavy-chain kinase / myosin heavy chain kinase activity / myosin II filament disassembly / ADP phosphatase activity / actomyosin contractile ring / actin crosslink formation / myosin II binding / AMP binding / actin filament bundle assembly / mitotic cytokinesis ...myosin-heavy-chain kinase / myosin heavy chain kinase activity / myosin II filament disassembly / ADP phosphatase activity / actomyosin contractile ring / actin crosslink formation / myosin II binding / AMP binding / actin filament bundle assembly / mitotic cytokinesis / cAMP binding / ADP binding / chemotaxis / actin filament binding / cell cortex / protein autophosphorylation / protein kinase activity / protein serine/threonine kinase activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Protein kinase-like fold / MHCK/EF2 kinase / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat ...Protein kinase-like fold / MHCK/EF2 kinase / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Barrel / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / Myosin heavy chain kinase A
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsYe, Q. / Jia, Z.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Characterization of the Catalytic and Nucleotide Binding Properties of the alpha-Kinase Domain of Dictyostelium Myosin-II Heavy Chain Kinase A.
Authors: Yang, Y. / Ye, Q. / Jia, Z. / Cote, G.P.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Data collection / Database references
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myosin heavy chain kinase A
B: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2288
Polymers69,2132
Non-polymers1,0156
Water3,459192
1
A: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1144
Polymers34,6071
Non-polymers5083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin heavy chain kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1144
Polymers34,6071
Non-polymers5083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.098, 109.960, 79.485
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 552 - 808 / Label seq-ID: 18 - 274

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Myosin heavy chain kinase A / MHCK-A


Mass: 34606.559 Da / Num. of mol.: 2 / Fragment: residues 552-841
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: mhkA, mhckA, DDB_G0291231 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42527, myosin-heavy-chain kinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 8000, sodium phosphate, Tris chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 23, 2007 / Details: White beam collimating mirror
RadiationMonochromator: Horizontally focusing monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.39→79.06 Å / Num. all: 277807 / Num. obs: 29130 / % possible obs: 99.8 % / Redundancy: 9.5 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 27.04
Reflection shellResolution: 2.39→2.49 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.66 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LKM

3lkm


Resolution: 2.39→79.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.461 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 1475 5.1 %RANDOM
Rwork0.1939 ---
obs0.1951 27601 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.5 Å2 / Biso mean: 42.152 Å2 / Biso min: 17.06 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å20 Å2-0 Å2
2--1.57 Å2-0 Å2
3---0.85 Å2
Refinement stepCycle: final / Resolution: 2.39→79.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3997 0 58 192 4247
Biso mean--53.5 39.61 -
Num. residues----503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194139
X-RAY DIFFRACTIONr_bond_other_d0.0030.023993
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9915593
X-RAY DIFFRACTIONr_angle_other_deg0.94739245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.545497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38725.233172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23115758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2891514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214523
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02889
X-RAY DIFFRACTIONr_mcbond_it2.8193.9692006
X-RAY DIFFRACTIONr_mcbond_other2.8153.9672005
X-RAY DIFFRACTIONr_mcangle_it4.6075.9262497
Refine LS restraints NCS

Ens-ID: 1 / Number: 15100 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.395→2.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 114 -
Rwork0.247 1841 -
all-1955 -
obs--91.31 %

+
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