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- PDB-3d6w: LytTr DNA-binding domain of putative methyl-accepting/DNA respons... -

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Basic information

Entry
Database: PDB / ID: 3d6w
TitleLytTr DNA-binding domain of putative methyl-accepting/DNA response regulator from Bacillus cereus.
ComponentsMethyl-accepting/DNA response regulator
KeywordsDNA BINDING PROTEIN / structural genomics / APC7590 / LytTr DNA-binding domain / methyl-accepting/DNA response regulator / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


LytTR signal transduction protein, putative / LytTr DNA-binding domain / LytTr DNA-binding domain / LytTR DNA-binding domain / LytTR-type HTH domain profile. / N-terminal domain of TfIIb - #10 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / N-terminal domain of TfIIb / Single Sheet / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...LytTR signal transduction protein, putative / LytTr DNA-binding domain / LytTr DNA-binding domain / LytTR DNA-binding domain / LytTR-type HTH domain profile. / N-terminal domain of TfIIb - #10 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / N-terminal domain of TfIIb / Single Sheet / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Methyl-accepting/DNA response regulator, putative
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsOsipiuk, J. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of LytTr DNA-binding domain of putative methyl-accepting/DNA response regulator from Bacillus cereus.
Authors: OSIPIUK, J. / EVDOKIMOVA, E. / KUDRITSKA, M. / SAVCHENKO, A. / EDWARDS, A.M. / JOACHIMIAK, A.
History
DepositionMay 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-accepting/DNA response regulator
B: Methyl-accepting/DNA response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8837
Polymers25,6812
Non-polymers2035
Water1,36976
1
A: Methyl-accepting/DNA response regulator
hetero molecules

A: Methyl-accepting/DNA response regulator
hetero molecules

B: Methyl-accepting/DNA response regulator
hetero molecules

B: Methyl-accepting/DNA response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,76714
Polymers51,3614
Non-polymers40510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area6670 Å2
ΔGint-47 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.784, 88.784, 74.425
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-39-

HOH

21A-65-

HOH

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Components

#1: Protein Methyl-accepting/DNA response regulator


Mass: 12840.362 Da / Num. of mol.: 2 / Fragment: LytTr DNA-binding domain, residues 106-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: BCE_1947 / Plasmid: pET15b modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q73A38
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.4 M magnesium chloride, 0.1 M HEPES buffer. Full length protein consisting of 214 original residues was used for crystallization. The obtained crystals contain only C-terminal domain of ...Details: 0.4 M magnesium chloride, 0.1 M HEPES buffer. Full length protein consisting of 214 original residues was used for crystallization. The obtained crystals contain only C-terminal domain of the protein, probably, due to proteolysis of the protein in crystallization conditions. , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→48 Å / Num. all: 12166 / Num. obs: 12166 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 27.8 % / Biso Wilson estimate: 65.6 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.804 / Net I/σ(I): 13.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 26.7 % / Rmerge(I) obs: 0.913 / Mean I/σ(I) obs: 4.4 / Num. unique all: 583 / Χ2: 0.934 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→48 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 14.485 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.3 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.209 581 4.8 %RANDOM
Rwork0.182 ---
all0.184 12141 --
obs0.184 12141 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.238 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 12 76 1866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221833
X-RAY DIFFRACTIONr_bond_other_d0.0020.021263
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9572474
X-RAY DIFFRACTIONr_angle_other_deg0.98433075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0015216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83123.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.14615320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.267158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
X-RAY DIFFRACTIONr_nbd_refined0.2130.2305
X-RAY DIFFRACTIONr_nbd_other0.2070.21200
X-RAY DIFFRACTIONr_nbtor_refined0.190.2833
X-RAY DIFFRACTIONr_nbtor_other0.0950.2987
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.080.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.25
X-RAY DIFFRACTIONr_mcbond_it1.3481.51314
X-RAY DIFFRACTIONr_mcbond_other0.1891.5436
X-RAY DIFFRACTIONr_mcangle_it1.70121774
X-RAY DIFFRACTIONr_scbond_it2.2223851
X-RAY DIFFRACTIONr_scangle_it3.2634.5700
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 40 -
Rwork0.255 837 -
all-877 -
obs-877 99.89 %
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)
115.76211.15947.970613.6469.925943.82640.13890.78930.4210.1812-0.6346-0.43190.61962.09920.4957-0.08650.00460.0749-0.1965-0.0063-0.1053-14.678344.526314.3315
24.2933.7807-3.14443.3296-2.76922.3032-0.2260.41320.04590.0980.6874-0.2058-0.0861-0.0234-0.4614-0.1472-0.0318-0.1183-0.1266-0.1536-0.1981-16.400842.228822.5964
315.7069-4.012710.90897.2365-5.53388.79130.3034-0.61720.94990.22980.26280.51290.24940.4769-0.5662-0.1491-0.0956-0.1229-0.132-0.1565-0.0988-15.840530.613218.1934
422.8156-13.01081.21337.4321-1.089612.70270.931.0625-0.063-1.6943-0.85230.3462-1.4829-0.8274-0.0777-0.21260.0984-0.13940.2355-0.2388-0.3675-13.078130.02267.0219
51.2705-1.5711-1.20461.96871.20964.17720.29270.661-0.06-0.3682-0.2180.1888-0.1818-0.0643-0.0746-0.20970.0693-0.1046-0.1014-0.0762-0.201-16.066537.564815.1209
610.56035.76381.12693.5927-0.76044.35410.20090.2005-0.06940.1908-0.1077-0.2041-0.5215-0.1822-0.0931-0.2691-0.0036-0.0667-0.0514-0.0779-0.151-3.713134.297317.7763
70.868-1.43590.2342.3754-0.38710.06310.1501-0.1393-0.05080.073-0.4210.0117-0.2680.04230.2709-0.166-0.0387-0.0963-0.0843-0.1301-0.2045-7.604230.56924.963
80.05910.05730.3874.30391.14292.67240.17590.02630.03790.2469-0.1178-0.0075-0.12050.1449-0.0581-0.31110.0537-0.1254-0.2045-0.1189-0.2165-15.843224.392125.0233
93.2781.3309-0.1930.5404-0.07830.0114-0.1950.31440.9932-0.02720.4227-0.5522-0.99260.1255-0.2277-0.11620.0819-0.2516-0.0659-0.2238-0.0576-17.527818.854225.4342
102.1925-2.0602-1.15721.93581.08740.61080.26990.0076-0.4883-0.1005-0.0646-0.00660.07180.1729-0.2054-0.2970.0159-0.1244-0.1842-0.12-0.1142-10.691820.283626.1361
1116.3192-0.78573.551836.60790.266712.42830.4916-0.80140.5778-1.1023-0.14311.9973-0.9433-0.3491-0.3485-0.1641-0.1162-0.06980.00970.1136-0.294212.820224.088536.352
121.35561.4529-0.5614.5444-5.05856.88260.2506-0.22390.07640.1595-0.7149-0.2653-0.45610.78020.4643-0.24960.0114-0.0337-0.08090.064-0.298216.986223.014437.6109
131.2827-5.1718-2.502721.927712.09298.6123-0.12070.15890.364-0.8132-0.1862-0.5902-0.64931.08140.3069-0.13470.1153-0.02640.0054-0.0285-0.179415.944125.144425.1954
147.27011.5328-2.29336.468-0.02011.84760.1505-0.1253-0.24880.1187-0.4689-0.0275-0.14870.29270.3184-0.17560.0911-0.0952-0.12160.0016-0.24816.162621.006127.2484
155.4828-6.31222.63557.8823-0.668310.3625-0.0007-0.3585-0.5780.3713-0.63410.2754-0.31010.28910.6348-0.27990.0673-0.0606-0.22070.066-0.20814.426519.992331.7092
160.42921.4079-0.11014.6185-0.3610.02820.6346-0.0737-0.0507-0.0451-0.80280.25330.0504-0.31160.1681-0.22050.0488-0.0484-0.1419-0.0049-0.17063.994325.239127.8816
172.3123-0.0938-0.15635.343-0.48752.08080.30490.45610.1225-0.104-0.42520.1584-0.01830.13160.1202-0.19760.0244-0.0286-0.1254-0.058-0.2739.980930.617921.6367
180.322-1.0494-1.00927.4286-2.004710.15570.530.82790.2435-1.1619-0.2538-0.65880.96660.3558-0.27620.06930.10210.12360.188-0.0426-0.229317.189534.5729.3621
1912.48794.3447-3.32671.5116-1.15740.88620.2195-0.5146-1.27640.2629-0.641-0.06230.12260.50960.42150.1090.16620.07970.191-0.03520.061720.000232.946615.9462
205.2157-4.39071.721718.4242-0.40944.31080.25930.67880.2377-1.6968-0.1014-0.16040.0569-0.024-0.1578-0.1340.0055-0.00840.0183-0.0205-0.290210.066533.793112.674
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA106 - 1181 - 13
2X-RAY DIFFRACTION2AA119 - 12614 - 21
3X-RAY DIFFRACTION3AA127 - 13122 - 26
4X-RAY DIFFRACTION4AA132 - 13627 - 31
5X-RAY DIFFRACTION5AA137 - 14932 - 44
6X-RAY DIFFRACTION6AA150 - 15745 - 52
7X-RAY DIFFRACTION7AA158 - 16753 - 62
8X-RAY DIFFRACTION8AA168 - 18363 - 78
9X-RAY DIFFRACTION9AA184 - 19479 - 89
10X-RAY DIFFRACTION10AA195 - 21490 - 109
11X-RAY DIFFRACTION11BB107 - 1142 - 9
12X-RAY DIFFRACTION12BB115 - 12310 - 18
13X-RAY DIFFRACTION13BB124 - 13319 - 28
14X-RAY DIFFRACTION14BB134 - 14229 - 37
15X-RAY DIFFRACTION15BB143 - 14838 - 43
16X-RAY DIFFRACTION16BB149 - 15844 - 53
17X-RAY DIFFRACTION17BB159 - 17654 - 71
18X-RAY DIFFRACTION18BB177 - 18772 - 82
19X-RAY DIFFRACTION19BB188 - 19583 - 90
20X-RAY DIFFRACTION20BB196 - 21591 - 110

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