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- PDB-3k0l: Crystal Structure of Putative MarR Family Transcriptional Regulat... -

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Basic information

Entry
Database: PDB / ID: 3k0l
TitleCrystal Structure of Putative MarR Family Transcriptional Regulator from Acinetobacter sp. ADP
ComponentsRepressor protein
KeywordsTranscription regulator / helix-turn-helix / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
MarR family / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...MarR family / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesAcinetobacter sp. ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.352 Å
AuthorsKim, Y. / Joachimiak, G. / Bigelow, L. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Putative MarR Family Transcriptional Regulator from Acinetobacter sp. ADP
Authors: Kim, Y. / Joachimiak, G. / Bigelow, L. / Cobb, G. / Joachimiak, A.
History
DepositionSep 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Repressor protein
B: Repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8293
Polymers36,7332
Non-polymers961
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-48 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.260, 80.544, 63.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Repressor protein / / Repressor protein of the Hydroxycinnamate (Hca) catabolic genes


Mass: 18366.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. ADP1 (bacteria) / Strain: ADPAdenosine diphosphate / Gene: hcaR, ACIAD1728 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q7X0D9
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.4 M Sodium Malonate pH 7.0, 0.1 M Bis-Tris Propane pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2009 / Details: mirrors
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: 2.35→49.8 Å / Num. all: 13890 / Num. obs: 13890 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 47.53 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.2
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 3.25 / Num. unique all: 673 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine: 1.4_162)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.352→49.75 Å / SU ML: 0.23 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.86 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1274 4.96 %random
Rwork0.183 ---
all0.187 25693 --
obs0.187 25693 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Solvent model: FLAT BULK SOLVENT MODEL. THE NUMBER OF TOTAL REFLECTIONS USED FOR REFINEMENT, INCLUDE BOTH F(+) AND F(-), IS 25693.
Bsol: 60.453 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3632 Å20 Å2-0 Å2
2--12.3938 Å20 Å2
3----11.0306 Å2
Refinement stepCycle: LAST / Resolution: 2.352→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 5 67 2324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132291
X-RAY DIFFRACTIONf_angle_d1.2683111
X-RAY DIFFRACTIONf_dihedral_angle_d19.129884
X-RAY DIFFRACTIONf_chiral_restr0.079372
X-RAY DIFFRACTIONf_plane_restr0.005403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3524-2.44660.32911480.25632673282199
2.4466-2.55790.31381340.239527252859100
2.5579-2.69280.32341520.222327032855100
2.6928-2.86150.331380.224227542892100
2.8615-3.08240.29131460.212527062852100
3.0824-3.39250.26841150.195827562871100
3.3925-3.88330.22431420.149327252867100
3.8833-4.89180.19491580.13412696285499
4.8918-49.7610.25291410.18862681282298
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)
1refined0.8405-0.21340.64710.6768-0.15361.6397-0.0920.07180.02230.00190.0263-0.0372-0.0284-0.185800.3907-0.02010.01420.40060.03120.415618.950117.179559.8152
21.1823-0.08630.28130.40080.36371.59010.0015-0.0660.05160.05180.00280.0416-0.1942-0.0023-0.00010.44380.00270.02350.39250.01540.4153
Refinement TLS groupSelection details: chain B

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