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- PDB-4hbl: Crystal structure of AbfR of Staphylococcus epidermidis -

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Basic information

Entry
Database: PDB / ID: 4hbl
TitleCrystal structure of AbfR of Staphylococcus epidermidis
ComponentsTranscriptional regulator, MarR familyTranscriptional regulation
KeywordsTRANSCRIPTION / HTH / Transcription factor / DNA binding
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
: / 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
Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsLiu, X. / Sun, X. / Gan, J. / Lan, L. / Yang, C.-G.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Oxidation-sensing Regulator AbfR Regulates Oxidative Stress Responses, Bacterial Aggregation, and Biofilm Formation in Staphylococcus epidermidis.
Authors: Liu, X. / Sun, X. / Wu, Y. / Xie, C. / Zhang, W. / Wang, D. / Chen, X. / Qu, D. / Gan, J. / Chen, H. / Jiang, H. / Lan, L. / Yang, C.G.
History
DepositionSep 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, MarR family
B: Transcriptional regulator, MarR family
C: Transcriptional regulator, MarR family
D: Transcriptional regulator, MarR family


Theoretical massNumber of molelcules
Total (without water)71,2664
Polymers71,2664
Non-polymers00
Water32418
1
A: Transcriptional regulator, MarR family
B: Transcriptional regulator, MarR family


Theoretical massNumber of molelcules
Total (without water)35,6332
Polymers35,6332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-59 kcal/mol
Surface area14980 Å2
MethodPISA
2
C: Transcriptional regulator, MarR family
D: Transcriptional regulator, MarR family


Theoretical massNumber of molelcules
Total (without water)35,6332
Polymers35,6332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-56 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.780, 50.616, 107.450
Angle α, β, γ (deg.)90.00, 110.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-203-

HOH

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Components

#1: Protein
Transcriptional regulator, MarR family / Transcriptional regulation


Mass: 17816.465 Da / Num. of mol.: 4 / Mutation: L44M, L72M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 35984 / RP62A / Gene: SERP2196 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HKZ1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.29 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M sodium acetate, 2.0M ammonium sulfate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 1, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 21526 / Num. obs: 20535 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 79.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 24.82 / SU ML: 0.265 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.935 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25883 1090 5.1 %RANDOM
Rwork0.21045 ---
all0.302 21526 --
obs0.21475 20399 95.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.551 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å21.26 Å2
2--4.69 Å2-0 Å2
3----2.79 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 0 18 4732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024795
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9686463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4855561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.42425.486257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.12115871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5531524
X-RAY DIFFRACTIONr_chiral_restr0.0960.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023592
LS refinement shellResolution: 2.502→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 56 -
Rwork0.311 1127 -
obs-1127 75.11 %
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)
12.19714.69174.223214.693910.759811.7835-0.1254-0.16060.22760.0078-0.24840.5375-0.0755-0.17230.37370.071-0.01520.06370.22480.01020.183254.850726.31527.9001
22.9602-0.21331.11750.7502-1.69054.64960.0384-0.78990.10810.2991-0.2829-0.0687-0.55780.27520.24440.2405-0.16850.04340.4256-0.06190.177264.531236.593753.4761
315.2147-5.6499-12.28133.19175.070810.3626-0.5251-1.0565-0.61010.23230.13660.07830.72280.57630.38850.4285-0.0986-0.00130.37740.07760.3654.372414.061936.2352
43.034-3.087-7.263.7878.635524.5395-0.0877-0.3758-0.07170.11310.0927-0.00420.53710.6656-0.0050.1309-0.03050.02320.22410.05970.12360.460621.001532.3192
51.9190.73270.02850.93610.11353.66750.02320.1434-0.0059-0.0484-0.0361-0.04930.1162-0.34710.01290.1385-0.002-0.02280.1465-0.01950.127359.080727.336110.3123
63.33276.4142-1.407124.34033.95694.40770.12470.1173-0.2124-0.7332-0.6183-0.0495-0.5361-0.61470.49360.1214-0.0274-0.02370.378-0.05590.401646.942623.612930.1289
72.4345-0.2522-1.98322.51093.230919.09330.3115-0.30080.2119-0.09110.1033-0.09280.0789-0.388-0.41480.0674-0.09340.01210.1518-0.01980.24481.428441.011926.2499
84.54260.84540.36211.3973-0.39440.2127-0.0842-0.3019-0.21290.21130.0671-0.0585-0.0571-0.10270.01720.1681-0.09190.00970.4780.05730.240793.407936.315139.8316
933.50447.854-16.00994.9664-3.313812.357-0.1107-0.23-1.4723-0.491-0.157-0.22850.84050.18060.26760.2750.0209-0.06450.009-0.00530.28785.057925.262118.5763
104.37242.1708-3.81116.5216-6.585614.37130.23350.0126-0.3981-0.4768-0.233-0.19840.13070.4934-0.00050.1198-0.0471-0.01630.1408-0.03190.24488.427733.294621.433
112.4730.23920.68450.7549-0.01292.6015-0.07520.11540.8221-0.0704-0.0614-0.0562-0.79530.28730.13670.5049-0.12430.07780.18570.02340.498887.665854.21269.8892
121.62992.51352.77414.25663.064112.0266-0.0691-0.17910.1518-0.263-0.16390.3397-0.4509-0.21440.2330.1953-0.0709-0.10060.2004-0.050.306474.081534.940416.2307
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 34
2X-RAY DIFFRACTION2A36 - 116
3X-RAY DIFFRACTION3A123 - 145
4X-RAY DIFFRACTION4B1 - 34
5X-RAY DIFFRACTION5B36 - 116
6X-RAY DIFFRACTION6B123 - 144
7X-RAY DIFFRACTION7C11 - 34
8X-RAY DIFFRACTION8C36 - 116
9X-RAY DIFFRACTION9C123 - 145
10X-RAY DIFFRACTION10D1 - 34
11X-RAY DIFFRACTION11D36 - 116
12X-RAY DIFFRACTION12D123 - 145

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