[English] 日本語
Yorodumi
- PDB-4mk6: Crystal Structure of Probable Dihydroxyacetone Kinase Regulator D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mk6
TitleCrystal Structure of Probable Dihydroxyacetone Kinase Regulator DHSK_reg from Listeria monocytogenes EGD-e
ComponentsProbable Dihydroxyacetone Kinase Regulator DHSK_reg
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Alpha-beta-fold / TetR-fold
Function / homology
Function and homology information


Transcriptional regulator TetR, C-terminal, Firmicutes type / Transcriptional regulator C-terminal region / : / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsKim, Y. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Probable Dihydroxyacetone Kinase Regulator DHSK_reg from Listeria monocytogenes EGD-e
Authors: Kim, Y. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable Dihydroxyacetone Kinase Regulator DHSK_reg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1533
Polymers22,0291
Non-polymers1242
Water59433
1
A: Probable Dihydroxyacetone Kinase Regulator DHSK_reg
hetero molecules

A: Probable Dihydroxyacetone Kinase Regulator DHSK_reg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3076
Polymers44,0582
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area3240 Å2
ΔGint-2 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.039, 77.039, 142.027
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-333-

HOH

-
Components

#1: Protein Probable Dihydroxyacetone Kinase Regulator DHSK_reg


Mass: 22029.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo0480 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8Y9P4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M magnesium chloride, 0.1 M HEPES pH 7.5, 15 %(v/v) ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 10941 / Num. obs: 10941 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 57.8 Å2 / Rsym value: 0.074 / Net I/σ(I): 12.6
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 516 / Rsym value: 0.725 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→30.193 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.24 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.232 523 4.79 %mixed
Rwork0.197 ---
all0.198 10929 --
obs0.198 10929 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.9 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 8 33 1565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031573
X-RAY DIFFRACTIONf_angle_d0.6172119
X-RAY DIFFRACTIONf_dihedral_angle_d14.391561
X-RAY DIFFRACTIONf_chiral_restr0.049231
X-RAY DIFFRACTIONf_plane_restr0.002268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3496-2.58590.27771430.25272504264799
2.5859-2.95980.25721200.226225652685100
2.9598-3.7280.23941250.208125922717100
3.728-30.19590.21611350.17842745288099
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)
15.9824-1.94192.24855.3714-2.26698.51990.3353-0.5087-1.0622-0.38180.14190.93360.9426-0.3351-0.50340.48860.006-0.08970.43590.19430.66175.105319.73223.5626
24.31644.9145-3.17385.6513-3.43882.8271-0.18090.6532-1.00150.63211.17071.43160.4009-1.2622-1.02140.7798-0.0105-0.07430.92220.40581.307623.096433.72591.7717
36.14520.79430.20544.85810.0833.29720.12230.00010.2567-0.07040.0835-0.129-0.38910.0116-0.23740.40490.05460.0090.30340.04610.251832.110927.61168.3506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 185 )

+
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