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- PDB-2rdp: The structure of a MarR family protein from Bacillus stearothermo... -

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Basic information

Entry
Database: PDB / ID: 2rdp
TitleThe structure of a MarR family protein from Bacillus stearothermophilus
Componentsputative transcriptional regulator MarR
KeywordsTRANSCRIPTION / MarR / transcriptional regulator / pfam PF01047 / winged-helix DNA binding motif / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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
BETA-MERCAPTOETHANOL / PHOSPHATE ION / Putative transcriptional regulator MarR
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsCuff, M.E. / Duggan, E. / Dementieva, I. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of a MarR family protein from Bacillus stearothermophilus.
Authors: Cuff, M.E. / Duggan, E. / Dementieva, I. / Moy, S. / Joachimiak, A.
History
DepositionSep 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Remark 999SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF DEPOSITION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative transcriptional regulator MarR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1716
Polymers17,8021
Non-polymers3695
Water1,40578
1
A: putative transcriptional regulator MarR
hetero molecules

A: putative transcriptional regulator MarR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,34212
Polymers35,6032
Non-polymers73810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.643, 73.643, 90.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein putative transcriptional regulator MarR


Mass: 17801.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: RBSTP1228 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D0VWY6*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.44 Å3/Da / Density % sol: 64.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.056M NaH2PO4, 1.344M K2HPO4, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97906 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 1, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionRedundancy: 6.7 % / Av σ(I) over netI: 9.2 / Number: 76259 / Rmerge(I) obs: 0.084 / Χ2: 2.03 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 11316 / % possible obs: 97.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955094.510.0677.1896.1
3.934.9598.710.0572.9346.9
3.443.9399.310.0632.0697.2
3.123.4499.110.0861.4767.3
2.93.129910.1391.3247.5
2.732.999.110.2281.1097.5
2.592.7398.410.3291.0097.4
2.482.5998.410.4651.0766.9
2.382.4897.210.5110.9745.8
2.32.3889.810.5871.0224.7
ReflectionResolution: 2.3→50 Å / Num. all: 11316 / Num. obs: 11316 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 61.2 Å2 / Rmerge(I) obs: 0.084 / Χ2: 2.025 / Net I/σ(I): 9.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1025 / Χ2: 1.022 / % possible all: 89.8

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.3 Å / D res low: 50 Å / FOM : 0.196 / FOM acentric: 0.235 / FOM centric: 0 / Reflection: 11231 / Reflection acentric: 9376 / Reflection centric: 1855
Phasing MAD setR cullis acentric: 1.95 / R cullis centric: 1 / Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 9376 / Reflection centric: 1855
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
13.92-501.150.50.32432
8.08-13.921.130.50.413487
5.7-8.082.710.50.2366150
4.4-5.71.750.30.2706214
3.58-4.41.230.10.11140270
3.02-3.582.620.101684330
2.61-3.025.920.102319375
2.3-2.612.01003003397
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se51.98842-0.062-0.253-0.1260
2Se38.92291-0.156-0.22-0.1270
3Se71.36843-0.385-0.299-0.0640
4Se87.78764-0.558-0.2060.0190
5Se113.40615-0.568-0.269-0.0260
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
13.92-500.2260.5260562432
8.08-13.920.3380.557022113487
5.7-8.080.3880.5470516366150
4.4-5.70.3930.5120920706214
3.58-4.40.3440.426014101140270
3.02-3.580.2550.305020141684330
2.61-3.020.1410.164026942319375
2.3-2.610.0510.058034003003397
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 11231
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.66-100650.587502
5.26-6.6664.20.851506
4.58-5.2662.80.883507
4.15-4.5862.10.877510
3.84-4.1560.70.886504
3.61-3.8463.30.849508
3.43-3.6161.70.845501
3.28-3.43630.843506
3.15-3.28640.819505
3.04-3.1568.50.814501
2.94-3.04630.807503
2.85-2.94700.802505
2.78-2.8572.30.735508
2.71-2.7874.30.79505
2.64-2.7174.20.753505
2.58-2.6478.80.733511
2.53-2.5879.60.749505
2.48-2.5381.40.724524
2.43-2.4881.50.757530
2.39-2.4381.70.737521
2.34-2.3981.50.709518
2.3-2.3487.30.627546

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.3→34.1 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.957 / SU ML: 0.172 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.207
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 544 4.8 %RANDOM
Rwork0.211 ---
all0.213 11228 --
obs0.213 11228 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.148 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å20 Å2
2---1.84 Å20 Å2
3---3.69 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 19 78 1245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221217
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9941637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1565146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2123.33363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37815244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6541516
X-RAY DIFFRACTIONr_chiral_restr0.0970.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02895
X-RAY DIFFRACTIONr_nbd_refined0.2060.2504
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2837
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.211
X-RAY DIFFRACTIONr_mcbond_it0.7921.5717
X-RAY DIFFRACTIONr_mcangle_it1.64821167
X-RAY DIFFRACTIONr_scbond_it2.8873509
X-RAY DIFFRACTIONr_scangle_it4.6354.5469
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 37 -
Rwork0.283 706 -
all-743 -
obs--90.28 %
Refinement TLS params.Method: refined / Origin x: 15.2433 Å / Origin y: 23.9272 Å / Origin z: 37.9395 Å
111213212223313233
T-0.1952 Å20.058 Å2-0.0277 Å2--0.2334 Å20.0095 Å2---0.1553 Å2
L2.3022 °21.1497 °21.5243 °2-3.1271 °20.3938 °2--2.3492 °2
S-0.1336 Å °0.1347 Å °0.1748 Å °-0.3567 Å °-0.0616 Å °0.3523 Å °-0.1498 Å °-0.0239 Å °0.1952 Å °

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