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- PDB-3he0: The Structure of a Putative Transcriptional Regulator TetR Family... -

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Basic information

Entry
Database: PDB / ID: 3he0
TitleThe Structure of a Putative Transcriptional Regulator TetR Family Protein from Vibrio parahaemolyticus.
ComponentsTranscriptional regulator, TetR family
Keywordstranscription regulator / TetR / AcrR / transcriptional regulator / Vibrio parahaemolyticus / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / Tetracyclin repressor-like HI_0893, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Cro/C1-type helix-turn-helix domain / : / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type ...: / Tetracyclin repressor-like HI_0893, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Cro/C1-type helix-turn-helix domain / : / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsCuff, M.E. / Hendricks, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The Structure of a Putative Transcriptional Regulator TetR Family Protein from Vibrio parahaemolyticus.
Authors: Cuff, M.E. / Hendricks, R. / Moy, S. / Joachimiak, A.
History
DepositionMay 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, TetR family
B: Transcriptional regulator, TetR family
C: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,83618
Polymers66,5413
Non-polymers1,29615
Water4,360242
1
A: Transcriptional regulator, TetR family
B: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,43314
Polymers44,3602
Non-polymers1,07212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-126 kcal/mol
Surface area17310 Å2
MethodPISA
2
C: Transcriptional regulator, TetR family
hetero molecules

C: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8088
Polymers44,3602
Non-polymers4476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4970 Å2
ΔGint-87 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.272, 95.548, 190.541
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsLikely a dimer, as formed by A and B in the asymmetric unit, and by C with its x,-y,-z symmetry mate.

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Components

#1: Protein Transcriptional regulator, TetR family


Mass: 22180.186 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VP0040 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q87TM9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS INDEED A DISCREPANCY BETWEEN THE PROTEIN STRUCTURE AND THE UNIPROT/UNP ENTRY. THE ELECTRON ...THERE IS INDEED A DISCREPANCY BETWEEN THE PROTEIN STRUCTURE AND THE UNIPROT/UNP ENTRY. THE ELECTRON DENSITY CLEARLY DISPLAYS AN R INSTEAD OF C IN ALL THREE MONOMERS OF THE ASYMMETRIC UNIT. THESE RESIDUE CODONS DIFFER IN ONE BASE. THIS IS LIKELY A SEQUENCING OR CLONING ERROR.

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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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8M ammonium sulfate,0.1M tri-sodium citrate, pH 7.5, 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: 0.97942, 0.97931
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979311
ReflectionRedundancy: 9.5 % / Av σ(I) over netI: 33.88 / Number: 329969 / Rmerge(I) obs: 0.089 / Χ2: 1.7 / D res high: 2.15 Å / D res low: 50 Å / Num. obs: 34848 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.835097.710.0616.0099.3
4.635.8398.810.0684.0199.4
4.054.6399.410.0663.5569.6
3.684.0599.410.0712.8929.7
3.413.6899.710.0692.0819.8
3.213.4199.810.0771.6369.9
3.053.2199.810.0871.3369.8
2.923.0599.810.1131.1259.9
2.812.9299.910.1391.0759.9
2.712.8110010.1661.0699.9
2.622.7110010.1990.9949.9
2.552.6210010.2310.95910
2.482.5510010.2530.9239.9
2.422.4810010.2950.8729.8
2.372.4210010.3330.8489.6
2.322.3710010.3840.8159.2
2.272.3210010.4290.8139
2.232.2710010.4860.8068.7
2.192.2310010.5510.7898.4
2.152.1999.910.580.7367.8
ReflectionResolution: 2.15→50 Å / Num. all: 34848 / Num. obs: 34848 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1.699 / Net I/σ(I): 33.882
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.58 / Num. unique all: 1762 / Χ2: 0.736 / % possible all: 99.9

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.15 Å / D res low: 50 Å / FOM : 0.293 / FOM acentric: 0.31 / FOM centric: 0.116 / Reflection: 34803 / Reflection acentric: 31683 / Reflection centric: 3120
Phasing MAD set

Highest resolution: 2.15 Å / Lowest resolution: 50 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.8610.20.200316833120
20.990.9619.125.50.240.21226622468
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
113.22-501.2110.90.60010872
17.62-13.221.22110.900529158
15.35-7.622.33110.4001285243
14.12-5.351.2410.50.4002419342
13.35-4.121.2610.30.2003884437
12.83-3.352.0210.20.1005673529
12.44-2.835.0210.10007849641
12.15-2.448.410.10009936698
213.22-500.870.8516.821.50.990.710872
27.62-13.220.920.9118.724.70.750.48529158
25.35-7.620.910.8414.719.60.790.551284242
24.12-5.350.980.9520.628.40.40.252417338
23.35-4.120.990.9721.830.50.250.173869433
22.83-3.350.990.9918.724.40.180.135606519
22.44-2.831118.324.30.110.087753631
22.15-2.441119.224.70.080.06109675
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se85.46245-0.828-0.854-0.0310
2Se77.18037-0.304-0.799-0.1620
3Se82.76672-0.386-0.368-0.1380
4Se115.33519-0.282-0.06-0.2270
5Se89.79949-0.886-0.35-0.1850
6Se72.49677-0.302-0.45-0.090
7Se106.65742-0.788-0.774-0.1840
8Se83.78969-0.447-0.292-0.0760
9Se59.26997-0.648-0.812-0.0060
10Se82.90631-0.846-0.348-0.0070
11Se108.85275-0.29-0.653-0.1540
12Se91.07994-0.167-0.462-0.1950
13Se71.81986-0.476-0.508-0.1940
14Se80.67454-0.984-0.157-0.0470
15Se92.1755-0.328-0.407-0.10
16Se81.50076-0.891-0.82-0.0690
17Se69.1389-0.828-0.854-0.031-0.064
18Se68.29311-0.304-0.799-0.162-0.064
19Se70.94778-0.386-0.368-0.138-0.06
20Se90.8536-0.281-0.06-0.227-0.041
21Se75.78542-0.887-0.35-0.184-0.041
22Se53.98891-0.302-0.449-0.09-0.035
23Se83.49982-0.788-0.774-0.184-0.037
24Se64.89809-0.447-0.292-0.075-0.03
25Se53.00464-0.649-0.812-0.006-0.012
26Se49.03548-0.847-0.347-0.007-0.019
27Se87.16106-0.289-0.653-0.153-0.022
28Se64.3568-0.167-0.462-0.195-0.03
29Se60.40377-0.473-0.509-0.194-0.02
30Se79.81557-0.984-0.157-0.047-0.022
31Se96.93533-0.326-0.408-0.1-0.009
32Se64.12686-0.89-0.819-0.069-0.01
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
13.22-500.5820.7280.36218010872
7.62-13.220.5870.6810.272687529158
5.35-7.620.6470.7040.34315281285243
4.12-5.350.550.60.19727612419342
3.35-4.120.4810.5180.1543213884437
2.83-3.350.3650.3910.08662025673529
2.44-2.830.2190.2330.04584907849641
2.15-2.440.0920.0980.004106349936698
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 34803
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.16-100550.722513
7.2-9.1649.40.902508
6.13-7.2430.891606
5.42-6.1345.60.884676
4.92-5.4250.50.894761
4.53-4.9249.20.927842
4.22-4.5345.80.916896
3.97-4.22510.909950
3.76-3.9754.20.8981017
3.58-3.7651.90.8931064
3.42-3.5851.80.8961125
3.28-3.4251.20.8931132
3.16-3.2855.80.8811223
3.05-3.16590.8721242
2.95-3.05590.8591282
2.86-2.9561.90.8491346
2.78-2.8661.70.8531356
2.7-2.7860.90.851382
2.63-2.767.30.8471459
2.57-2.6368.70.851465
2.51-2.5770.30.8311513
2.45-2.51720.8321556
2.4-2.4576.30.8341582
2.35-2.478.60.8231602
2.3-2.3577.50.8471665
2.26-2.377.70.821659
2.22-2.2680.70.8081702
2.15-2.2282.50.7472679

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.005data 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: MAD / Resolution: 2.2→48.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.881 / SU B: 11.554 / SU ML: 0.132 / SU R Cruickshank DPI: 0.258 / SU Rfree: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.196
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1649 5 %RANDOM
Rwork0.187 ---
all0.189 ---
obs0.189 32866 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.29 Å2 / Biso mean: 29.556 Å2 / Biso min: 7.76 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å20 Å20 Å2
2---1.47 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4295 0 73 242 4610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224463
X-RAY DIFFRACTIONr_bond_other_d0.0010.023003
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9596025
X-RAY DIFFRACTIONr_angle_other_deg0.91437300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2725551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51724.753223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14815780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1341531
X-RAY DIFFRACTIONr_chiral_restr0.0830.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02899
X-RAY DIFFRACTIONr_mcbond_it0.7881.52727
X-RAY DIFFRACTIONr_mcbond_other0.181.51118
X-RAY DIFFRACTIONr_mcangle_it1.51124327
X-RAY DIFFRACTIONr_scbond_it2.58431736
X-RAY DIFFRACTIONr_scangle_it4.0954.51695
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 127 -
Rwork0.229 2233 -
all-2360 -
obs--99.75 %
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)
10.26721.1618-0.08078.3015-0.58270.94220.18230.0471-0.01080.6222-0.0426-0.02540.08430.0069-0.13970.2679-0.09510.04190.2152-0.05030.135818.378211.662737.3043
24.701-0.66374.06298.4187-0.04149.70390.02910.869-0.2221-0.9483-0.0687-0.56450.46390.80820.03960.4221-0.19110.09120.31710.01140.246822.735812.446526.4802
33.20420.7803-0.90163.9687-0.32594.84250.1022-0.1524-0.21640.462-0.15740.05720.2938-0.08290.05520.1742-0.04820.04750.208-0.00570.200521.092430.245728.3783
46.55150.67411.56265.57411.40749.49190.0598-0.34630.26350.6042-0.0780.3575-0.1293-0.43120.01820.20220.03140.08810.1533-0.02160.207222.630340.258732.3778
517.9580.6831-0.808211.5135-2.88217.95170.073-0.2898-0.23270.24130.1773-0.03430.3842-0.0241-0.25030.6020.103-0.14030.15530.01640.250249.93218.855233.5496
60.5793-2.25731.20319.9797-4.56723.8924-0.0581-0.0804-0.06690.69140.1534-0.2450.41210.0905-0.09520.51460.0765-0.15390.19380.03290.272450.724613.465437.0251
72.6408-0.41180.46893.31490.64371.72470.0563-0.2099-0.22920.55830.0788-0.02470.22560.0407-0.13510.2454-0.0014-0.01880.08510.01710.102340.531532.552929.9304
84.03570.03550.31993.9152-1.84354.4929-0.00850.4963-0.3578-0.36230.15650.28110.5077-0.4499-0.1480.1402-0.04930.00190.1566-0.0140.125129.559131.931219.1125
98.47343.3297-1.3729.67240.68436.199-0.25470.1039-0.9015-0.52370.2661-0.6650.27660.4114-0.01140.1767-0.0320.04990.1654-0.13450.286442.29813.2314-7.514
103.80421.90381.09961.18870.4830.6871-0.03990.0343-0.0866-0.04940.1043-0.1965-0.10030.0595-0.06440.1563-0.0220.02770.1191-0.03080.152224.189914.7021-6.0437
116.8409-0.0067-0.08583.48831.94446.86080.2991-1.2893-0.72440.8007-0.1727-0.16570.41340.1943-0.12640.2247-0.1319-0.01030.30780.0580.443628.615610.65533.4283
121.8990.50050.0083.46590.0262.10820.01480.0165-0.0681-0.09580.0223-0.21330.15610.0956-0.03710.13690.02250.00860.10290.02640.11079.67855.6587-3.487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 99
2X-RAY DIFFRACTION2A100 - 126
3X-RAY DIFFRACTION3A127 - 174
4X-RAY DIFFRACTION4A175 - 193
5X-RAY DIFFRACTION5B8 - 26
6X-RAY DIFFRACTION6B27 - 77
7X-RAY DIFFRACTION7B78 - 165
8X-RAY DIFFRACTION8B166 - 193
9X-RAY DIFFRACTION9C8 - 42
10X-RAY DIFFRACTION10C43 - 97
11X-RAY DIFFRACTION11C98 - 126
12X-RAY DIFFRACTION12C127 - 193

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