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- PDB-3e6m: The crystal structure of a MarR family transcriptional regulator ... -

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Basic information

Entry
Database: PDB / ID: 3e6m
TitleThe crystal structure of a MarR family transcriptional regulator from Silicibacter pomeroyi DSS.
ComponentsMarR family Transcriptional regulator
Keywordstranscription regulator / APC88769 / MarR / Silicibacter pomeroyi DSS / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / DNA-binding / Plasmid / Transcription / Transcription regulation
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 speciesSilicibacter pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsTan, K. / Volkart, L. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a MarR family transcriptional regulator from Silicibacter pomeroyi DSS.
Authors: Tan, K. / Volkart, L. / Freeman, L. / Joachimiak, A.
History
DepositionAug 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: 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: MarR family Transcriptional regulator
B: MarR family Transcriptional regulator
C: MarR family Transcriptional regulator
D: MarR family Transcriptional regulator
E: MarR family Transcriptional regulator
F: MarR family Transcriptional regulator
G: MarR family Transcriptional regulator
H: MarR family Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)142,1528
Polymers142,1528
Non-polymers00
Water8,737485
1
A: MarR family Transcriptional regulator
B: MarR family Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)35,5382
Polymers35,5382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-46 kcal/mol
Surface area14720 Å2
MethodPISA
2
C: MarR family Transcriptional regulator
D: MarR family Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)35,5382
Polymers35,5382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-46 kcal/mol
Surface area14540 Å2
MethodPISA
3
E: MarR family Transcriptional regulator
F: MarR family Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)35,5382
Polymers35,5382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-47 kcal/mol
Surface area14760 Å2
MethodPISA
4
G: MarR family Transcriptional regulator
H: MarR family Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)35,5382
Polymers35,5382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-48 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.433, 93.198, 101.556
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAuthors state that the biological unit is experimentally unknown. The chains A and B, C and D, E and F, G and H are expected to form dimers, respectively.

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Components

#1: Protein
MarR family Transcriptional regulator


Mass: 17769.008 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Strain: DSS / Gene: SPOA0451 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5LLB9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 20% PEG1000, 0.1M Phosphate-citrate 0.2M Li2SO4, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2007 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.486
ReflectionResolution: 2.2→39.6 Å / Num. obs: 136295 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.54 / Num. unique all: 3027 / % possible all: 84.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→39.6 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was solved in space group P212121 and refined in space group P21 with the application of a twin law of "h,-k,-l".
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 6965 5.11 %randon
Rwork0.1849 ---
all0.1874 136295 --
obs0.1874 136295 96.06 %-
Displacement parametersBiso mean: -13.7642 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-15.6703 Å21.5849 Å2
2--23.6588 Å20 Å2
3----15.6703 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9047 0 0 485 9532
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_refined_d0.008
X-RAY DIFFRACTIONf_angle_refined_deg1.223
LS refinement shellResolution: 2.193→2.23 Å
RfactorNum. reflection% reflection
Rfree0.317 285 -
Rwork0.323 --
obs-5328 0.98 %
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)
1-0.04930.3370.28420.5264-0.12590.49920.05420.03150.1663-0.05830.0880.2628-0.00490.2791-0.06260.3069-0.015-0.00950.5247-0.01420.36823.13111.811616.5354
20.01610.10640.15150.2032-0.01530.09570.0498-0.1290.07620.0861-0.0258-0.06370.00960.02720.01680.4016-0.00020.01480.4899-0.01590.358319.8974-4.147543.4392
30.0327-0.0096-0.0097-0.00290.02540.09860.1066-0.20810.08750.01530.10610.0776-0.0063-0.1244-0.10650.30320.00110.04540.6954-0.04890.39587.2405-5.181528.5269
40.03880.0678-0.04980.09650.00260.13210.06-0.04560.1233-0.0050.05380.04730.14370.0342-0.04260.40640.0910.01160.466-0.06790.439122.7122-13.932318.821
5-0.0081-0.14270.08390.1964-0.06670.1946-0.1247-0.2728-0.01720.24440.29280.0181-0.02880.1069-0.05950.4080.09490.06840.4944-0.01780.363525.4847-5.417126.6684
60.0678-0.1388-0.15410.3894-0.02280.36190.014-0.0260.10950.11380.07090.0216-0.19750.3655-0.06790.4307-0.06550.0310.5462-0.11760.409930.848416.824312.9696
70.05970.0142-0.02270.07530.04110.1294-0.0229-0.07660.00140.04010.0780.00720.0850.3773-0.02890.35290.1315-0.00610.7106-0.0070.293340.5173-0.094214.5291
80.45890.13390.07320.1365-0.03080.4153-0.02680.25140.1528-0.16610.11130.06830.1540.088-0.040.34320.0725-0.02210.50940.01830.386521.1176-6.205610.9182
90.0258-0.16120.22970.4930.07310.45040.0608-0.18060.01710.04590.0383-0.3179-0.0287-0.2295-0.05740.2822-0.01320.00250.4601-0.03990.363152.26171.786748.7189
100.07090.00520.04040.1262-0.0850.16260.02210.08730.0864-0.10350.00950.00830.1432-0.27230.00560.4187-0.04960.01030.53160.04610.364555.5456-4.185921.8054
110.04050.0224-0.00170.0418-0.02210.07030.16560.04040.03470.0139-0.0425-0.015-0.04460.1461-0.03910.3717-0.01930.07740.64770.04940.477768.0732-5.402136.7026
120.05350.0421-0.00030.1107-0.07890.0685-0.0192-0.0089-0.05640.032-0.0523-0.0959-0.01430.022-0.10110.2905-0.1664-0.0256-0.01060.10230.348652.7408-14.006246.4514
130.10090.0225-0.03140.17770.09330.0335-0.00880.08570.0761-0.11290.0892-0.18540.0115-0.06630.15650.3047-0.18580.1118-0.00690.0610.355749.9054-5.247638.2979
140.30170.02050.16510.31250.03140.32130.0242-0.04020.1488-0.1657-0.1895-0.0045-0.0955-0.21650.06060.32870.04750.01640.39970.06660.339144.866716.889152.5681
150.23280.19770.12370.1227-0.0970.14970.01450.0691-0.04210.05080.1332-0.0161-0.0029-0.2548-0.05580.3112-0.1594-0.03020.56750.00450.27534.9378-0.13850.6734
161.0092-0.3029-0.11720.08830.11040.91630.0777-0.13880.30830.0644-0.04960.01910.18640.02470.01350.4361-0.10070.01720.71020.05150.444654.2719-6.349654.3717
170.02330.109-0.17920.14770.06010.04520.0580.0235-0.1048-0.02450.0001-0.00920.045-0.0635-0.06750.37190.12510.00030.4547-0.02620.358214.68533.574767.3436
180.46690.0796-0.05060.1875-0.1240.43430.10220.1496-0.05190.1021-0.11590.0237-0.1527-0.02640.00620.2791-0.02720.00240.362-0.02720.252617.95049.40794.1837
190.2893-0.16210.09110.1919-0.13810.2278-0.07880.1541-0.1164-0.0181-0.2942-0.16740.04310.2220.25320.386-0.08390.01040.53520.01350.510230.48210.70379.489
20-0.00060.0095-0.0043-0.0632-0.02750.23550.0692-0.14640.0068-0.05940.1244-0.0496-0.1484-0.2625-0.05230.39070.08520.04750.5838-0.01060.337514.105419.224871.2871
210.2704-0.05750.0368-0.0606-0.08410.1350.0923-0.1562-0.0377-0.0189-0.0623-0.0271-0.2399-0.3988-0.03520.28330.05140.02240.527-0.02480.180312.258510.819177.5257
220.33820.03230.05210.358-0.10010.3016-0.1515-0.011-0.12670.04080.1831-0.09050.0875-0.21020.00940.3773-0.03250.03020.45470.04310.41066.9233-11.261463.85
230.23380.01340.00630.03130.00640.21230.04070.07960.01320.00470.02830.08220.1055-0.3111-0.0560.3677-0.0082-0.00990.69660.02410.3628-2.84845.732465.3779
240.22830.077-0.00180.20350.0990.49640.01670.0851-0.0425-0.1667-0.0598-0.0344-0.2291-0.14940.04460.39790.02730.0130.4540.03350.31316.350311.698661.576
250.2432-0.072-0.02860.29-0.13120.25250.1346-0.039-0.0757-0.04440.05940.01240.1347-0.0408-0.10820.3451-0.0859-0.0040.4031-0.01550.3286-14.80663.651199.4195
260.278-0.06260.07050.22980.14010.30020.0376-0.1894-0.0266-0.1333-0.0879-0.0209-0.20940.07750.02440.3627-0.01080.01530.4870.00230.2971-17.76519.600572.4471
270.62240.00940.03430.61170.1733-0.07850.0256-0.10840.0223-0.1196-0.2240.0969-0.0427-0.15370.140.30770.03220.02610.3643-0.01230.4189-30.497910.792487.3634
280.0580.00520.0333-0.00680.01740.08330.13560.07630.0632-0.01030.04030.0529-0.09780.0373-0.11030.4133-0.02780.05580.58530.05150.3548-13.91919.06995.6561
290.1057-0.0855-0.09630.04220.00930.0785-0.09620.1908-0.04560.16330.02650.0164-0.14280.23760.05820.3774-0.0350.00460.6320.02140.2728-12.326810.661388.9999
300.3030.1225-0.0750.26-0.00940.0416-0.1653-0.0557-0.1915-0.13780.1577-0.05610.10210.07960.03880.4416-0.00620.03040.4180.00470.4839-7.0552-11.2555103.0508
310.69870.1561-0.10370.10890.18330.8649-0.0421-0.06380.1923-0.01140.02930.03980.1170.3453-0.00360.4178-0.0547-0.00880.5714-0.05720.44532.78295.7816101.3382
320.11-0.0267-0.040.2178-0.06340.0349-0.0128-0.0747-0.02490.0491-0.06410.05570.01270.08230.00730.35280.0178-0.01190.3828-0.02410.3248-16.458911.788105.2315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 8:46
2X-RAY DIFFRACTION2chain A and resid 47:113
3X-RAY DIFFRACTION3chain A and resid 114:135
4X-RAY DIFFRACTION4chain A and resid 136:156
5X-RAY DIFFRACTION5chain B and resid 10:46
6X-RAY DIFFRACTION6chain B and resid 47:113
7X-RAY DIFFRACTION7chain B and resid 114:135
8X-RAY DIFFRACTION8chain B and resid 136:158
9X-RAY DIFFRACTION9chain C and resid 8:46
10X-RAY DIFFRACTION10chain C and resid 47:113
11X-RAY DIFFRACTION11chain C and resid 114:135
12X-RAY DIFFRACTION12chain C and resid 136:156
13X-RAY DIFFRACTION13chain D and resid 10:46
14X-RAY DIFFRACTION14chain D and resid 47:113
15X-RAY DIFFRACTION15chain D and resid 114:135
16X-RAY DIFFRACTION16chain D and resid 136:158
17X-RAY DIFFRACTION17chain E and resid 8:46
18X-RAY DIFFRACTION18chain E and resid 47:113
19X-RAY DIFFRACTION19chain E and resid 114:135
20X-RAY DIFFRACTION20chain E and resid 136:158
21X-RAY DIFFRACTION21chain F and resid 10:46
22X-RAY DIFFRACTION22chain F and resid 47:113
23X-RAY DIFFRACTION23chain F and resid 114:135
24X-RAY DIFFRACTION24chain F and resid 136:158
25X-RAY DIFFRACTION25chain G and resid 8:46
26X-RAY DIFFRACTION26chain G and resid 47:113
27X-RAY DIFFRACTION27chain G and resid 114:135
28X-RAY DIFFRACTION28chain G and resid 136:158
29X-RAY DIFFRACTION29chain H and resid 10:46
30X-RAY DIFFRACTION30chain H and resid 47:113
31X-RAY DIFFRACTION31chain H and resid 114:135
32X-RAY DIFFRACTION32chain H and resid 136:158

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