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- PDB-4rgr: Crystal Structure of Putative MarR Family Transcriptional Regulat... -

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Basic information

Entry
Database: PDB / ID: 4rgr
TitleCrystal Structure of Putative MarR Family Transcriptional Regulator HcaR from Acinetobacter sp. ADP
ComponentsRepressor protein
KeywordsTRANSCRIPTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / winged helix-turn-helix
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
4'-HYDROXYCINNAMIC ACID / Repressor protein
Similarity search - Component
Biological speciesAcinetobacter sp. ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.302 Å
AuthorsKim, Y. / Joachimiak, G. / Bigelow, L. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2014
Title: Crystal Structure of Putative MarR Family Transcriptional Regulator HcaR from Acinetobacter sp. ADP
Authors: Kim, Y. / Joachimiak, G. / Bigelow, L. / Cobb, G. / Joachimiak, A.
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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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)37,3467
Polymers36,7332
Non-polymers6135
Water2,108117
1
A: Repressor protein
B: Repressor protein
hetero molecules

A: Repressor protein
B: Repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,69114
Polymers73,4664
Non-polymers1,22510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area16940 Å2
ΔGint-137 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.017, 83.626, 63.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsto generate tetramer apply x,y,z and -x+1,-y,z to the asymmetric unit of dimer

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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) / Gene: ACIAD1728, hcaR / Plasmid: pMCSG19c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q7X0D9
#2: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID / P-Coumaric acid


Mass: 164.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
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, 5 mM coumaric acid, 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: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 15489 / Num. obs: 15489 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 44.06 Å2 / Rsym value: 0.09 / Net I/σ(I): 14.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 747 / Rsym value: 0.499 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXCDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.302→39.576 Å / SU ML: 0.24 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.213 767 4.97 %random
Rwork0.172 ---
all0.174 15439 --
obs0.174 15439 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.5 Å2
Refinement stepCycle: LAST / Resolution: 2.302→39.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 40 117 2306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022371
X-RAY DIFFRACTIONf_angle_d0.6183219
X-RAY DIFFRACTIONf_dihedral_angle_d18.447929
X-RAY DIFFRACTIONf_chiral_restr0.04372
X-RAY DIFFRACTIONf_plane_restr0.003416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3019-2.47960.24011490.19362816296598
2.4796-2.72910.24921500.197829133063100
2.7291-3.12390.2621470.197929273074100
3.1239-3.93520.21611510.168329683119100
3.9352-39.58160.18671700.1573048321899
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)
11.99152.03252.64963.14582.67683.5596-0.59031.3193-1.2904-3.66741.17110.1331-1.1410.2551-0.77890.9456-0.040300.5437-0.13090.684437.20888.883731.0765
24.52390.1370.18598.80155.24427.0079-0.2520.05260.2732-0.24610.33540.0561-0.2656-0.1892-0.12470.2089-0.05830.01920.2612-0.00240.255140.715721.005448.2615
37.46130.51851.46685.5529-0.18146.7519-0.31680.4069-0.3254-0.15990.2135-0.4332-0.00820.84440.0480.2237-0.03940.03850.3674-0.040.305256.059117.810760.9207
46.51035.5642-2.46294.7893-2.1561.00470.77470.6008-1.49720.5112-0.6261.76791.74660.51710.19791.44280.1331-0.03630.8652-0.22161.602867.52465.061169.7193
57.66081.89965.71120.74470.71714.6213-0.0239-0.5833-0.409-0.01610.04630.0334-0.0355-0.3144-0.01110.2343-0.01170.06280.3608-0.03710.339640.3416.126762.173
65.26364.5677-5.52947.9226-3.53887.0664-0.5512-1.0925-1.0805-0.18070.0824-0.36230.23220.83960.33530.3343-0.0665-0.00420.3541-0.02130.205842.80052.892448.5796
78.5831-0.98660.35943.23362.3693.29080.6337-2.7573-1.27771.8371-0.04880.66070.35621.0472-0.22440.5705-0.09990.130.67320.0480.46139.88986.671559.517
81.1265-0.2917-1.04383.8646-2.5399.27140.096-0.01740.0019-0.222-0.2883-0.4317-0.42440.7980.23190.3678-0.11880.04440.2842-0.04960.302549.797515.480738.0727
96.0848-3.6877-0.0872.4804-0.57372.17650.7359-0.36550.2801-0.1251-0.73040.6206-0.8007-0.84640.01410.9394-0.01880.02440.4974-0.02430.52639.898627.38133.9631
107.7087-0.33-0.55076.66875.51564.50280.24160.62721.1427-0.2399-0.5924-0.1396-1.1246-0.00690.53771.16040.0230.0320.46090.110.520547.507129.700925.1653
111.3111-1.33780.38489.7127-6.11643.76610.43010.3384-0.2658-0.9444-0.7259-0.11720.79750.64050.10740.5366-0.09230.05720.3876-0.04790.359448.637210.151228.1737
124.1984-0.4706-1.37313.9262.64575.18740.17840.246-0.2489-0.9055-0.2175-0.02350.0514-0.54450.01860.3326-0.09520.01230.23550.01630.211835.71876.777741.0347
138.68726.18686.82045.69836.01686.3959-0.80292.79581.8268-2.12930.0673-0.1495-2.53952.31850.04130.7761-0.17650.0730.77530.16740.655533.672725.737847.0703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 98 )
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 130 )
6X-RAY DIFFRACTION6chain 'A' and (resid 131 through 150 )
7X-RAY DIFFRACTION7chain 'B' and (resid 11 through 16 )
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 54 )
9X-RAY DIFFRACTION9chain 'B' and (resid 55 through 70 )
10X-RAY DIFFRACTION10chain 'B' and (resid 71 through 104 )
11X-RAY DIFFRACTION11chain 'B' and (resid 105 through 125 )
12X-RAY DIFFRACTION12chain 'B' and (resid 126 through 147 )
13X-RAY DIFFRACTION13chain 'B' and (resid 148 through 153 )

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