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- PDB-3q9s: Crystal structure of rra(1-215) from Deinococcus Radiodurans -

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Basic information

Entry
Database: PDB / ID: 3q9s
TitleCrystal structure of rra(1-215) from Deinococcus Radiodurans
ComponentsDNA-binding response regulator
KeywordsDNA BINDING PROTEIN / response regulator
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA-binding response regulator
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsLiu, Y. / Gao, Z.Q. / Dong, Y.H. / Ji, C.N.
CitationJournal: To be Published
Title: Crystal structure of rra(1-215) from Deinococcus Radiodurans
Authors: Liu, Y. / Gao, Z.Q. / Dong, Y.H. / Ji, C.N.
History
DepositionJan 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)28,4721
Polymers28,4721
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.542, 98.542, 54.447
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein DNA-binding response regulator


Mass: 28472.008 Da / Num. of mol.: 1 / Fragment: N-terminal residues 1-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_2418 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RRR8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 14% PEG4000, 16% 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 13487 / Num. obs: 13149 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 48.4 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.435 / Num. unique all: 661 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→32.255 Å / SU ML: 0.32 / σ(F): 1.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 1097 4.88 %RANDOM
Rwork0.2073 ---
all0.21 11243 --
obs0.21 11243 97.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.763 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso mean: 59.2931 Å2
Baniso -1Baniso -2Baniso -3
1-4.5899 Å20 Å2-0 Å2
2--4.5899 Å20 Å2
3----9.1798 Å2
Refinement stepCycle: LAST / Resolution: 2.4→32.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 0 52 1720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041706
X-RAY DIFFRACTIONf_angle_d0.8472310
X-RAY DIFFRACTIONf_dihedral_angle_d16.218664
X-RAY DIFFRACTIONf_chiral_restr0.054267
X-RAY DIFFRACTIONf_plane_restr0.004305
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.50930.29781260.25092722284899
2.5093-2.64150.34531280.23062702283099
2.6415-2.80690.28211700.22722746291699
2.8069-3.02350.27091480.20362679282799
3.0235-3.32750.25531240.21032760288499
3.3275-3.80830.25911580.1882676283499
3.8083-4.79560.21321310.15652683281498
4.7956-32.25830.24031120.21952420253287
Refinement TLS params.Method: refined / Origin x: -10.5948 Å / Origin y: 39.7752 Å / Origin z: 7.306 Å
111213212223313233
T0.2113 Å20.0063 Å20.0186 Å2-0.2756 Å2-0.0038 Å2--0.3471 Å2
L1.9072 °20.8785 °2-0.2607 °2-3.0531 °2-1.6625 °2--0.9148 °2
S0.0407 Å °-0.1539 Å °-0.4331 Å °-0.0436 Å °-0.0197 Å °0.1906 Å °-0.0184 Å °-0.0439 Å °-0.0214 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 212
2X-RAY DIFFRACTION1allA216 - 267

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