[English] 日本語
Yorodumi
- PDB-3hyj: Crystal structure of the N-terminal LAGLIDADG domain of DUF199/WhiA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hyj
TitleCrystal structure of the N-terminal LAGLIDADG domain of DUF199/WhiA
ComponentsProtein DUF199/WhiA
KeywordsTRANSCRIPTION REGULATOR / LAGLIDADG / homing endonuclease / helix-turn-helix / HTH
Function / homology
Function and homology information


regulation of sporulation / cell cycle / cell division / DNA binding
Similarity search - Function
Sporulation regulator WhiA / Sporulation transcription regulator WhiA, N-terminal domain / Sporulation regulator WhiA, C-terminal / WhiA, LAGLIDADG-like domain / WhiA C-terminal HTH domain / WhiA N-terminal LAGLIDADG-like domain / WhiA LAGLIDADG-like domain / Homing endonucleases / Endonuclease I-creI / Homing endonuclease ...Sporulation regulator WhiA / Sporulation transcription regulator WhiA, N-terminal domain / Sporulation regulator WhiA, C-terminal / WhiA, LAGLIDADG-like domain / WhiA C-terminal HTH domain / WhiA N-terminal LAGLIDADG-like domain / WhiA LAGLIDADG-like domain / Homing endonucleases / Endonuclease I-creI / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Probable cell division protein WhiA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.6 Å
AuthorsKaiser, B.K. / Clifton, M.C. / Shen, B.W. / Stoddard, B.L.
CitationJournal: Structure / Year: 2009
Title: The structure of a bacterial DUF199/WhiA protein: domestication of an invasive endonuclease.
Authors: Kaiser, B.K. / Clifton, M.C. / Shen, B.W. / Stoddard, B.L.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Protein DUF199/WhiA
D: Protein DUF199/WhiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4727
Polymers46,1942
Non-polymers2785
Water1,02757
1
A: Protein DUF199/WhiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2123
Polymers23,0971
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Protein DUF199/WhiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2604
Polymers23,0971
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.448, 79.899, 115.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein DUF199/WhiA


Mass: 23097.018 Da / Num. of mol.: 2
Fragment: N-terminal domain, generated by proteolytic digestion of the full-length protein (UNP residues 1 to 198)
Source method: isolated from a genetically manipulated source
Details: the expressed protein does not contain any affinity tags.
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: MSB8, TM_1708 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9X234
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Tris, 9.0, 20% Ethanol, 200 mM NaCl. Crystals of the N-terminal domain were generated by the addition of trypsin to the full-length protein just prior to setting crystal drops., VAPOR ...Details: 0.1 M Tris, 9.0, 20% Ethanol, 200 mM NaCl. Crystals of the N-terminal domain were generated by the addition of trypsin to the full-length protein just prior to setting crystal drops., VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: R-AXIS IV++ / Detector: IMAGE PLATE / Date: Jul 30, 2008 / Details: mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 15039 / Num. obs: 14107 / % possible obs: 93.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 18.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 6.35 / % possible all: 89

-
Processing

Software
NameVersionClassification
d*TREKdata scaling
PHASERphasing
REFMAC5.5.0072refinement
Hdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→40.19 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 24.914 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.894 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26038 712 5.1 %RANDOM
Rwork0.19823 ---
obs0.20132 13375 94.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.642 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2---0.14 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 15 57 3066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223061
X-RAY DIFFRACTIONr_bond_other_d0.0010.022076
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9754131
X-RAY DIFFRACTIONr_angle_other_deg1.07635051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2015382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45623.095126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15315533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3531520
X-RAY DIFFRACTIONr_chiral_restr0.1040.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02656
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_it0.5351.51911
X-RAY DIFFRACTIONr_mcbond_other0.0851.5775
X-RAY DIFFRACTIONr_mcangle_it1.00523069
X-RAY DIFFRACTIONr_scbond_it1.41631150
X-RAY DIFFRACTIONr_scangle_it2.4254.51061
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.604→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 53 -
Rwork0.291 988 -
obs--95.68 %
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)
12.05850.6528-0.01454.80090.2193.16560.10080.05330.0974-0.3148-0.002-0.0029-0.31290.0283-0.09880.2875-0.02960.10220.0107-0.03750.20019.21730.12117.234
22.4816-0.16860.02913.56571.55573.92780.0032-0.2425-0.16810.08810.1812-0.18920.080.0654-0.18440.2503-0.01720.01470.0333-0.00080.19189.59424.31433.144
34.20370.5065-0.61662.46010.59623.8252-0.0072-0.26690.00270.35350.1144-0.01470.10310.2112-0.10720.3095-0.04390.0080.0478-0.01240.145822.94641.3228.047
42.11190.0839-1.07412.93460.62793.9156-0.0126-0.01880.0325-0.10220.13780.0178-0.10760.1751-0.12520.33480.00230.00040.0127-0.00980.225126.16841.296-5.243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 98
2X-RAY DIFFRACTION2A99 - 192
3X-RAY DIFFRACTION3D1 - 77
4X-RAY DIFFRACTION4D78 - 193

+
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