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

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Basic information

Entry
Database: PDB / ID: 4rgx
TitleCrystal Structure of Putative MarR Family Transcriptional Regulator HcaR from Acinetobacter sp. ADP complexed with 3,4-dihydroxy bezoic acid
ComponentsRepressor protein
KeywordsTRANSCRIPTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / winged helix-turn-helix
Function / homology
Function and homology information


response to stress / 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
3,4-DIHYDROXYBENZOIC ACID / Repressor protein
Similarity search - Component
Biological speciesAcinetobacter sp. ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.102 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 complexed with 3,4-dihydroxy bezoic acid
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)37,2368
Polymers36,7332
Non-polymers5036
Water3,279182
1
A: Repressor protein
B: Repressor protein
hetero molecules

A: Repressor protein
B: Repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,47316
Polymers73,4664
Non-polymers1,00712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area16830 Å2
ΔGint-89 kcal/mol
Surface area25340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.584, 83.105, 63.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-355-

HOH

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-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
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, 5 mM 3,4-dihydroxy bezoic 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: Jul 17, 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: 2.1→50 Å / Num. all: 20059 / Num. obs: 20059 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 35.09 Å2 / Rsym value: 0.098 / Net I/σ(I): 12.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 983 / Rsym value: 0.638 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXCDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.102→34.784 Å / SU ML: 0.2 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.63 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1014 5.11 %random
Rwork0.171 ---
all0.173 19862 --
obs0.173 19862 98.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.2 Å2
Refinement stepCycle: LAST / Resolution: 2.102→34.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 32 182 2369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072292
X-RAY DIFFRACTIONf_angle_d0.923110
X-RAY DIFFRACTIONf_dihedral_angle_d15.393891
X-RAY DIFFRACTIONf_chiral_restr0.058367
X-RAY DIFFRACTIONf_plane_restr0.004403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1016-2.21240.27241440.21962552269697
2.2124-2.3510.27141440.21762639278398
2.351-2.53250.24351470.176926612808100
2.5325-2.78720.23011440.184426812825100
2.7872-3.19030.25661480.185227022850100
3.1903-4.01850.2091390.157227502889100
4.0185-34.78840.18531480.154828633011100
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)
17.1481-5.00154.13085.3567-0.85824.6047-1.4927-0.5978-2.2262.81511.1402-0.6998-0.2576-0.04750.37640.80350.0948-0.02420.83940.04880.795527.29578.493363.3892
23.1742-0.43611.32399.289-6.0394.2532-0.2083-0.09040.1920.52450.2840.1078-0.4397-0.0385-0.02230.25750.06380.02870.2725-0.01040.270322.729120.919845.7761
39.14713.24322.18947.9522.9686.8301-0.0932-0.1383-0.3697-0.0887-0.1045-0.20250.03220.03070.17130.21890.02950.03990.30060.03760.305613.874319.090433.2659
42.70023.41712.25135.72751.37353.44290.1067-0.9256-0.87380.766-0.03210.05271.0829-0.74660.05450.42950.03860.06610.54390.11710.47636.067712.831938.2481
57.08311.0392-0.5165.3339-0.72589.1402-0.369-0.2816-0.07140.19320.12450.5348-0.1292-0.50350.20.23610.0915-0.01060.40150.04050.32874.766821.13329.9011
65.5361-4.3185-4.85524.45951.79227.9009-0.9838-0.322-3.6018-0.8081-0.0705-1.41332.6042-0.79761.09711.382-0.1990.08310.81720.11871.4786-3.4914.174724.923
78.8735-1.00275.04810.64180.02013.40510.03210.61-0.1861-0.1432-0.0871-0.0709-0.11890.24230.00870.27160.03040.06460.37370.03090.296520.732616.847430.0784
84.33130.4237-1.61323.929-0.08033.3594-0.18980.4384-0.33760.18280.11970.0140.1643-0.14530.13370.29410.0704-0.02520.27780.03910.236224.75754.664545.3751
98.4952-4.0329-1.062.76763.19518.67091.24223.2072-1.3113-2.2543-1.9407-1.50210.5228-0.05410.42760.71070.24640.16370.8194-0.04520.762524.00225.363234.9261
101.0842-0.561-1.91593.15783.8819.45850.03910.0659-0.01310.2211-0.33430.3129-0.151-0.69740.31160.39320.0690.04660.34590.05720.326513.415715.488557.6169
112.8764-0.4588-0.8168.81450.41772.56350.76670.72450.5288-0.8313-0.7543-1.2609-1.00721.1860.1240.8839-0.08770.13910.4820.04290.649323.607927.257260.4885
124.83321.7704-4.85252.3318-1.85654.860.58060.38881.2617-0.013-0.37790.1713-1.3333-0.651-0.57040.97660.09420.03620.5408-0.00880.648114.020231.484864.8169
134.27220.7332.22788.77230.32398.3647-0.0048-1.71852.55130.1215-0.4639-0.7652-1.09090.65960.43760.915-0.11550.04930.5791-0.11060.776220.385228.285274.5158
141.74830.76020.48676.34645.08634.03090.2286-0.4091-0.22190.9308-0.48680.14430.6679-0.46460.28470.52630.06550.07120.49380.09120.366115.244310.137467.048
154.18972.918-2.7573.2478-3.74854.66060.22050.00740.14490.7632-0.1280.141-0.25930.3329-0.11090.33270.06920.02730.3336-0.01560.281628.491710.034252.4174
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 54 )
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 70 )
5X-RAY DIFFRACTION5chain 'A' and (resid 71 through 91 )
6X-RAY DIFFRACTION6chain 'A' and (resid 92 through 98 )
7X-RAY DIFFRACTION7chain 'A' and (resid 99 through 125 )
8X-RAY DIFFRACTION8chain 'A' and (resid 126 through 149 )
9X-RAY DIFFRACTION9chain 'B' and (resid 11 through 16 )
10X-RAY DIFFRACTION10chain 'B' and (resid 17 through 54 )
11X-RAY DIFFRACTION11chain 'B' and (resid 55 through 70 )
12X-RAY DIFFRACTION12chain 'B' and (resid 71 through 83 )
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 104 )
14X-RAY DIFFRACTION14chain 'B' and (resid 105 through 125 )
15X-RAY DIFFRACTION15chain 'B' and (resid 126 through 152 )

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