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- PDB-3dpj: The crystal structure of a TetR transcription regulator from Sili... -

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Basic information

Entry
Database: PDB / ID: 3dpj
TitleThe crystal structure of a TetR transcription regulator from Silicibacter pomeroyi DSS
ComponentsTranscription regulator, TetR family
KeywordsDNA BINDING PROTEIN / APC88616 / TetR / Silicibacter pomeroyi DSS / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / 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
Transcription regulator, TetR family
Similarity search - Component
Biological speciesSilicibacter pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsTan, K. / Li, H. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a TetR transcription regulator from Silicibacter pomeroyi DSS
Authors: Tan, K. / Li, H. / Freeman, L. / Joachimiak, A.
History
DepositionJul 8, 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

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Assembly

Deposited unit
A: Transcription regulator, TetR family
B: Transcription regulator, TetR family
C: Transcription regulator, TetR family
D: Transcription regulator, TetR family
E: Transcription regulator, TetR family
F: Transcription regulator, TetR family
G: Transcription regulator, TetR family
H: Transcription regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,77446
Polymers175,3508
Non-polymers3,42438
Water14,484804
1
E: Transcription regulator, TetR family
F: Transcription regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,66211
Polymers43,8372
Non-polymers8259
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint10 kcal/mol
Surface area17600 Å2
MethodPISA
2
G: Transcription regulator, TetR family
H: Transcription regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,66211
Polymers43,8372
Non-polymers8259
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint6 kcal/mol
Surface area17210 Å2
MethodPISA
3
C: Transcription regulator, TetR family
D: Transcription regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,97316
Polymers43,8372
Non-polymers1,13514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint21 kcal/mol
Surface area18190 Å2
MethodPISA
4
A: Transcription regulator, TetR family
B: Transcription regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4768
Polymers43,8372
Non-polymers6396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint4 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.523, 93.072, 93.397
Angle α, β, γ (deg.)89.35, 71.02, 71.04
Int Tables number1
Space group name H-MP1
DetailsThe chains A and B, C and D, E and F, G and H form dimers, respectively.

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Components

#1: Protein
Transcription regulator, TetR family


Mass: 21918.748 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Strain: DSS / Gene: SPO1902 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5LS67
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.7 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 289 K / pH: 8.5
Details: 0.2M Sodium Citrate, 0.1M Tris 15% PEG 400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2007 / Details: MIRROR
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
Reflection twinOperator: h,h-k,h-l / Fraction: 0.502
ReflectionResolution: 1.9→42 Å / Num. obs: 138074 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 1.77 / % possible all: 86.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→41.61 Å / Phase error: 35.25 / Stereochemistry target values: ENGH & HUBER
Details: The structure was resolved in space group C2 and was refined in space group P1 with a twin-law of "h, h-k, h-l".
RfactorNum. reflection% reflection
Rfree0.243 14106 5.28 %
Rwork0.193 --
obs0.196 266959 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.95 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 50.08 Å2
Baniso -1Baniso -2Baniso -3
1-6.548 Å20.162 Å20.142 Å2
2---5.977 Å2-6.689 Å2
3----8.585 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11958 0 216 804 12978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812376
X-RAY DIFFRACTIONf_angle_d1.0916670
X-RAY DIFFRACTIONf_dihedral_angle_d19.6594452
X-RAY DIFFRACTIONf_chiral_restr0.0671830
X-RAY DIFFRACTIONf_plane_restr0.0042166
LS refinement shellResolution: 1.9→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 570 -
Rwork0.311 9926 -
obs--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)
10.4-0.1327-0.08640.2377-0.00070.05160.06150.1192-0.2065-0.4058-0.0781-0.34910.06150.0547-0.00610.36990.09760.10090.2766-0.01910.442918.4884-14.2417-14.0849
20.8373-0.15790.21511.2062-0.76531.08840.01930.0805-0.04540.7056-0.0235-0.5775-0.43710.20370.04730.2849-0.0537-0.11830.08490.02490.271910.54172.32515.4903
30.7798-0.0419-0.11760.6313-0.06780.49350.0037-0.0446-0.0118-0.2086-0.07050.02660.2114-0.34460.06730.2245-0.0701-0.06720.2228-0.04260.1765-17.3286-13.0544-15.3078
40.3478-0.23050.28661.63330.35610.4808-0.0626-0.0051-0.01850.37510.06530.20250.0901-0.1142-0.02690.30410.05180.04840.16830.02240.1579-11.10574.98412.8383
50.9512-0.5161-0.58470.64760.11490.1928-0.1244-0.2304-0.0606-0.25020.1667-0.33940.02950.2083-0.03870.29130.06560.10570.345-0.07690.427948.572224.889929.5486
60.81120.22630.1250.0335-0.04171.28840.0460.0255-0.08150.03710.065-0.1066-0.43950.236-0.05520.2794-0.0757-0.02120.1299-0.00290.160741.069541.520849.2431
70.2950.2620.09720.24420.0453-0.09410.0566-0.02390.3915-0.10620.02190.20420.1207-0.2127-0.023-0.3281-0.26480.01580.29790.07010.252912.683626.541828.7926
80.197-0.03080.60980.5179-0.58262.0017-0.0402-0.0643-0.04480.27660.09080.131-0.727-0.6016-0.09120.36310.16340.04120.24810.0250.133719.556644.629246.9318
90.7805-0.255-0.51020.22060.27170.8321-0.0094-0.27090.08120.0597-0.05560.1066-0.3344-0.1656-0.01820.32230.12050.13380.3192-0.02790.222-18.179352.332810.6579
100.5047-0.0943-0.23821.41050.0338-0.78140.05120.10240.0222-0.5317-0.04060.197-0.028-0.1154-0.01930.3541-0.0082-0.08260.19580.03490.1258-11.143334.6058-7.7839
110.72120.15880.09890.6862-0.06410.3228-0.0249-0.00470.17670.3617-0.0251-0.4899-0.2080.13990.06310.3563-0.0706-0.1630.26460.00990.407616.78653.26689.6258
120.57120.45480.2658-0.11780.01970.84150.0259-0.0136-0.1877-0.3372-0.0809-0.34410.1070.08570.07390.41480.03670.10120.09580.02550.232110.473537.2815-10.1282
130.7742-0.1424-0.68210.25590.30690.88460.0308-0.27840.09460.1165-0.00810.133-0.3248-0.2018-0.03940.41380.14090.1080.396-0.01640.279212.050891.516854.523
140.42030.0922-0.69480.959-0.42771.388-0.05570.17160.0459-0.50540.07640.20170.6174-0.5501-0.06020.438-0.106-0.08980.19380.03370.084219.206673.772636.1988
150.4681-0.17630.24220.1238-0.05620.3688-0.1935-0.09840.19710.20030.0704-0.2728-0.27150.12880.12470.2931-0.0559-0.16230.2512-0.03160.339547.005692.714853.4292
160.36340.56490.07340.9293-0.04870.77730.0275-0.0352-0.1505-0.773-0.1415-0.56370.2520.17250.1280.54470.07340.1630.1220.05430.285840.81976.762933.6738
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 47
2X-RAY DIFFRACTION2A48 - 191
3X-RAY DIFFRACTION3B2 - 47
4X-RAY DIFFRACTION4B48 - 191
5X-RAY DIFFRACTION5C-2 - 47
6X-RAY DIFFRACTION6C48 - 191
7X-RAY DIFFRACTION7D2 - 47
8X-RAY DIFFRACTION8D48 - 191
9X-RAY DIFFRACTION9E-1 - 47
10X-RAY DIFFRACTION10E48 - 191
11X-RAY DIFFRACTION11F3 - 47
12X-RAY DIFFRACTION12F48 - 190
13X-RAY DIFFRACTION13G-1 - 47
14X-RAY DIFFRACTION14G48 - 191
15X-RAY DIFFRACTION15H3 - 47
16X-RAY DIFFRACTION16H48 - 190

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