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- PDB-6jq1: Crystal Structure of DdrO from Deinococcus geothermalis -

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Basic information

Entry
Database: PDB / ID: 6jq1
TitleCrystal Structure of DdrO from Deinococcus geothermalis
ComponentsTranscriptional regulator, XRE family
KeywordsDNA BINDING PROTEIN / Transcription factor / Xre / HTH / Dimerization
Function / homology
Function and homology information


Helix-turn-helix domain / : / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
: / Transcriptional regulator, XRE family
Similarity search - Component
Biological speciesDeinococcus geothermalis DSM 11300 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsLu, H. / Hua, Y. / Zhao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870051 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structure and DNA damage-dependent derepression mechanism for the XRE family member DG-DdrO.
Authors: Lu, H. / Wang, L. / Li, S. / Pan, C. / Cheng, K. / Luo, Y. / Xu, H. / Tian, B. / Zhao, Y. / Hua, Y.
History
DepositionMar 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, XRE family
B: Transcriptional regulator, XRE family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8977
Polymers29,8622
Non-polymers355
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-50 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.950, 127.900, 156.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Transcriptional regulator, XRE family


Mass: 14930.978 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus geothermalis DSM 11300 (bacteria)
Strain: DSM 11300 / Gene: Dgeo_0336 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q1J1J5
#2: Chemical
ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Li
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7 / Details: LiCl, HEPES

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 16314 / % possible obs: 98.7 % / Redundancy: 4.67 % / Biso Wilson estimate: 57.15 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.88
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.48 % / Rmerge(I) obs: 0.692 / Num. unique obs: 1177 / % possible all: 96.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PU7

4pu7


Resolution: 2.3→30 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.06
RfactorNum. reflection% reflection
Rfree0.2595 834 5.12 %
Rwork0.2368 --
obs0.238 16283 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 5 8 2081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042104
X-RAY DIFFRACTIONf_angle_d0.722845
X-RAY DIFFRACTIONf_dihedral_angle_d21.348811
X-RAY DIFFRACTIONf_chiral_restr0.294322
X-RAY DIFFRACTIONf_plane_restr0.004365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3031-2.44740.36511370.35512508X-RAY DIFFRACTION98
2.4474-2.63620.37311290.31692562X-RAY DIFFRACTION100
2.6362-2.90120.33891350.30842570X-RAY DIFFRACTION99
2.9012-3.32050.27871350.28692604X-RAY DIFFRACTION100
3.3205-4.18120.25291320.22132607X-RAY DIFFRACTION99
4.1812-28.10230.22581660.19482598X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 12.6293 Å / Origin y: 30.2647 Å / Origin z: 58.6735 Å
111213212223313233
T0.489 Å20.094 Å20.0183 Å2-0.5448 Å20.0055 Å2--0.3898 Å2
L1.1107 °21.6021 °20.1193 °2-3.4663 °2-0.0363 °2--1.7915 °2
S-0.0902 Å °0.2081 Å °0.0102 Å °0.0321 Å °0.0619 Å °0.0667 Å °0.0231 Å °0.0834 Å °0.0188 Å °
Refinement TLS groupSelection details: all

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