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

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Basic information

Entry
Database: PDB / ID: 4rgs
TitleCrystal Structure of Putative MarR Family Transcriptional Regulator HcaR from Acinetobacter sp. ADP complexed with Vanilin
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
4-hydroxy-3-methoxybenzaldehyde / Repressor protein
Similarity search - Component
Biological speciesAcinetobacter sp. ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.298 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 Vanilin
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)37,4148
Polymers36,7332
Non-polymers6816
Water1,54986
1
A: Repressor protein
B: Repressor protein
hetero molecules

A: Repressor protein
B: Repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,82716
Polymers73,4664
Non-polymers1,36112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area16250 Å2
ΔGint-158 kcal/mol
Surface area26170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.679, 82.816, 63.026
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-307-

HOH

Detailsto generate tetramer apply x,y,z and -x+2,-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-V55 / 4-hydroxy-3-methoxybenzaldehyde


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
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, 5mM Vanilin, 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 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: 2.298→50 Å / Num. all: 15395 / Num. obs: 15395 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 44.29 Å2 / Rsym value: 0.098 / Net I/σ(I): 10.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 3.46 / Num. unique all: 738 / Rsym value: 0.674 / % 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: 2.298→39.401 Å / SU ML: 0.28 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.99 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.225 766 4.99 %random
Rwork0.165 ---
all0.167 15337 --
obs0.167 15337 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.5 Å2
Refinement stepCycle: LAST / Resolution: 2.298→39.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 0 44 86 2287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072302
X-RAY DIFFRACTIONf_angle_d13118
X-RAY DIFFRACTIONf_dihedral_angle_d17.185895
X-RAY DIFFRACTIONf_chiral_restr0.067365
X-RAY DIFFRACTIONf_plane_restr0.005401
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.298-2.47540.30151350.2122850298599
2.4754-2.72450.26391660.191228533019100
2.7245-3.11860.24831760.179828553031100
3.1186-3.92850.20931380.161729583096100
3.9285-39.40650.20411510.14933055320699
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)
13.85991.61160.99435.926-0.86686.26010.114-0.8611-1.00312.13240.5303-0.7657-0.6663-0.1495-0.10450.73190.0794-0.05710.52340.05640.616758.30978.740863.5147
22.7748-0.34521.39423.7082-2.60217.8892-0.2176-0.03110.28290.5308-0.0323-0.0975-1.02010.55080.10090.30740.02920.00230.31450.01860.341654.662820.861746.3506
36.66040.4544-0.55234.65340.26926.4909-0.2445-0.0141-0.46390.02350.10010.27870.432-0.80240.020.20740.01920.0140.40690.01470.305641.457615.327636.0756
44.36560.4028-0.65975.3034-1.66229.1404-0.36660.0551-0.05660.53980.75060.7201-1.1632-1.4676-0.00730.43860.1601-0.0020.57310.10340.36935.256422.57533.7817
55.77552.43590.95945.25480.74064.8943-0.44741.4161-0.4085-0.729-0.10170.8744-1.07-0.237-0.18130.32970.157-0.09290.6935-0.02750.426738.001518.586323.7241
62.12921.7279-0.03981.5189-0.37053.5196-0.0355-0.33750.9341-1.15520.5630.20890.0011-0.7797-0.15991.89880.2249-0.01160.8248-0.06051.751827.41754.138323.8497
73.6254-1.46213.09261.1228-0.22523.3208-0.22520.6223-0.6099-0.20560.1649-0.1004-0.34040.56670.14340.2607-0.01340.08330.38190.02650.302152.125816.845230.1329
82.0487-0.09970.39473.5085-0.70123.1365-0.39010.5312-0.3032-0.03290.1383-0.01630.4038-0.0856-0.05730.29430.0506-0.01510.24830.00090.241256.18074.749745.5424
95.6674-2.7160.11687.56240.72272.54450.64511.8181-0.1444-1.9744-1.4903-0.08320.99620.13890.90120.6340.1910.0680.674-0.01390.412555.70146.383134.9832
102.5294-0.7344-2.60672.02591.50378.9373-0.14630.1028-0.0410.2077-0.14220.27470.0893-0.9370.24830.35050.01930.04080.32910.00880.290444.383312.341552.6613
119.28761.89523.21689.19440.07767.7368-0.0273-0.86860.7839-0.2186-0.18750.6149-0.6328-0.59550.25240.46820.03760.05730.2636-0.05460.271247.553421.040165.3537
126.5291-0.1146-0.69067.2633-0.11296.94390.30550.20890.8803-0.588-0.2524-0.4584-1.61370.25760.07010.7758-0.04830.01440.4103-0.04370.547651.305629.311362.4472
136.28841.73452.24333.00091.44871.32050.0106-1.73552.23280.2244-0.4664-1.395-1.2505-0.66850.41520.8692-0.08450.04870.4536-0.03320.626250.780527.612974.5272
141.2281.2524-0.0022.58181.97172.21150.251-0.3638-0.36921.0026-0.5383-0.06810.8988-0.67140.11490.57610.07340.00980.51880.07840.363546.93279.952266.3876
153.85812.0158-0.56716.0856-2.5913.41760.2186-0.30370.18150.4743-0.5099-0.0703-0.25560.41490.27360.30860.04830.01030.3507-0.02380.250159.98210.076252.5678
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 70 )
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 83 )
5X-RAY DIFFRACTION5chain 'A' and (resid 84 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 150 )
9X-RAY DIFFRACTION9chain 'B' and (resid 11 through 16 )
10X-RAY DIFFRACTION10chain 'B' and (resid 17 through 39 )
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 54 )
12X-RAY DIFFRACTION12chain 'B' and (resid 55 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 153 )

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