[English] 日本語
Yorodumi
- PDB-1mfw: STRUCTURE OF N-TERMINAL DOUBLECORTIN DOMAIN FROM DCLK: SELENOMETH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mfw
TitleSTRUCTURE OF N-TERMINAL DOUBLECORTIN DOMAIN FROM DCLK: SELENOMETHIONINE LABELED PROTEIN
ComponentsDOUBLECORTIN-LIKE KINASE (N-TERMINAL DOMAIN)
KeywordsTRANSFERASE / Doublecortin / Doublecortin-like kinase / Microtubule bundling / Cortex development
Function / homology
Function and homology information


central nervous system projection neuron axonogenesis / axon extension / negative regulation of protein localization to nucleus / dendrite morphogenesis / endosomal transport / protein localization to nucleus / forebrain development / neuron projection morphogenesis / central nervous system development / neuron migration ...central nervous system projection neuron axonogenesis / axon extension / negative regulation of protein localization to nucleus / dendrite morphogenesis / endosomal transport / protein localization to nucleus / forebrain development / neuron projection morphogenesis / central nervous system development / neuron migration / response to virus / nervous system development / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Doublecortin domain / Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Doublecortin domain / Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase DCLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsKim, M.H. / Cierpickil, T. / Derewenda, U. / Krowarsch, D. / Feng, Y. / Devedjiev, Y. / Dauter, Z. / Walsh, C.A. / Otlewski, J. / Bushweller, J.H. / Derewenda, Z.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: The DCX-domain Tandems of Doublecortin and Doublecortin-like Kinase
Authors: Kim, M.H. / Cierpickil, T. / Derewenda, U. / Krowarsch, D. / Feng, Y. / Devedjiev, Y. / Dauter, Z. / Walsh, C.A. / Otlewski, J. / Bushweller, J.H. / Derewenda, Z.
History
DepositionAug 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DOUBLECORTIN-LIKE KINASE (N-TERMINAL DOMAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4443
Polymers12,2521
Non-polymers1922
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.785, 29.430, 40.099
Angle α, β, γ (deg.)90.00, 115.72, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe Biological Assembly is a Tandem of N-terminal and C-terminal domains

-
Components

#1: Protein DOUBLECORTIN-LIKE KINASE (N-TERMINAL DOMAIN) / Doublecortin


Mass: 12251.792 Da / Num. of mol.: 1 / Fragment: (N-Terminal Domain), Residues 49-154 / Mutation: L120(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGSTUNIL / Production host: Escherichia coli (E. coli) / References: UniProt: O15075
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.7 Å3/Da / Density % sol: 27.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5
Details: CITRATE BUFFER, AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / PH range low: 5.8 / PH range high: 5.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
22.2-2.4 Mammonium sulfate1reservoir
30.1 Msodium citrate1reservoirpH5.2-5.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9795,0.9791,0.9718
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 29, 2002 / Details: Double crystal focusing mirrors
RadiationMonochromator: SI (III) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97911
30.97181
ReflectionResolution: 1.6→22.82 Å / Num. obs: 9312 / % possible obs: 84.6 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.038 / Net I/σ(I): 32.5
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.21 / Rsym value: 0.032 / % possible all: 35.9
Reflection
*PLUS
Highest resolution: 1.6 Å / Redundancy: 3 % / Num. measured all: 28275
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.66 Å / % possible obs: 35.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.2

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MAD / Resolution: 1.6→10 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.169 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.679 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18046 838 9.1 %RANDOM
Rwork0.12745 ---
obs0.13212 9256 98.61 %-
all-9312 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.464 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å20 Å20.6 Å2
2---0.89 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 0 10 134 999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022879
X-RAY DIFFRACTIONr_bond_other_d0.0060.02794
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9741186
X-RAY DIFFRACTIONr_angle_other_deg0.88331852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8015105
X-RAY DIFFRACTIONr_chiral_restr0.1040.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02951
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02183
X-RAY DIFFRACTIONr_nbd_refined0.2430.2159
X-RAY DIFFRACTIONr_nbd_other0.2660.2940
X-RAY DIFFRACTIONr_nbtor_other0.0820.2521
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.240
X-RAY DIFFRACTIONr_mcbond_it1.2591.5527
X-RAY DIFFRACTIONr_mcangle_it2.1422856
X-RAY DIFFRACTIONr_scbond_it2.4183352
X-RAY DIFFRACTIONr_scangle_it3.744.5330
X-RAY DIFFRACTIONr_rigid_bond_restr1.4972879
X-RAY DIFFRACTIONr_sphericity_bonded1.8412865
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 24
Rwork0.204 238
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.18 / Rfactor Rwork: 0.127
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

+
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