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- PDB-3mn2: The crystal structure of a probable AraC family transcriptional r... -

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Basic information

Entry
Database: PDB / ID: 3mn2
TitleThe crystal structure of a probable AraC family transcriptional regulator from Rhodopseudomonas palustris CGA009
Componentsprobable AraC family transcriptional regulator
Keywordstranscription regulator / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
Transcription regulator HTH, AraC- type, ligand binding domain-like / AraC-binding-like domain / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / Homeobox-like domain superfamily ...Transcription regulator HTH, AraC- type, ligand binding domain-like / AraC-binding-like domain / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Probable transcriptional regulator, AraC family
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsTan, K. / Li, H. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a probable AraC family transcriptional regulator from Rhodopseudomonas palustris CGA009
Authors: Tan, K. / Li, H. / Buck, K. / Joachimiak, A.
History
DepositionApr 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: probable AraC family transcriptional regulator
B: probable AraC family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6554
Polymers24,4652
Non-polymers1902
Water2,540141
1
A: probable AraC family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4223
Polymers12,2321
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: probable AraC family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)12,2321
Polymers12,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.097, 64.097, 88.088
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsExperimentally unknown. The molecule is likely monomeric.

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Components

#1: Protein probable AraC family transcriptional regulator


Mass: 12232.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA0567 / Plasmid: pMCSG19B / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q6NCA5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Phosphate-citrate 40% v/v PEG300, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 10, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.8→21 Å / Num. all: 18976 / Num. obs: 18976 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 42.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 3.2 / Num. unique all: 954 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→20.981 Å / SU ML: 0.26 / σ(F): 0.02 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 943 5.1 %random
Rwork0.1985 ---
all0.2009 18473 --
obs0.2009 18473 96.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.521 Å2 / ksol: 0.383 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→20.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 10 141 1851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071760
X-RAY DIFFRACTIONf_angle_d12377
X-RAY DIFFRACTIONf_dihedral_angle_d16.127655
X-RAY DIFFRACTIONf_chiral_restr0.064254
X-RAY DIFFRACTIONf_plane_restr0.004311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7995-1.89430.27521290.23952320X-RAY DIFFRACTION90
1.8943-2.01290.25711350.22722461X-RAY DIFFRACTION96
2.0129-2.16820.27551530.20272503X-RAY DIFFRACTION98
2.1682-2.38610.25731450.19742549X-RAY DIFFRACTION99
2.3861-2.73070.27851320.19562566X-RAY DIFFRACTION99
2.7307-3.43790.23811410.19662576X-RAY DIFFRACTION100
3.4379-20.98210.21651080.18932555X-RAY DIFFRACTION96
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.5102-0.9162-0.87461.53611.43171.55720.0801-0.11120.29270.02390.1408-0.2120.03330.0676-0.21740.1747-0.00630.03560.14190.00360.21826.47844.681320.6078
21.7961-0.5312-1.45941.84941.45091.49440.1022-0.0250.0587-0.14730.0063-0.0445-0.1464-0.0215-0.05590.13010.01620.00070.1585-0.02340.1155
Refinement TLS groupSelection details: chain B

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