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- PDB-3mvp: The Crystal Structure of a TetR/AcrR transcriptional regulator fr... -

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Basic information

Entry
Database: PDB / ID: 3mvp
TitleThe Crystal Structure of a TetR/AcrR transcriptional regulator from Streptococcus mutans to 1.85A
ComponentsTetR/AcrR transcriptional regulator
Keywordstranscription regulator / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homology
Function and homology information


Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative transcriptional regulator (TetR/AcrR family)
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsStein, A.J. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of a TetR/AcrR transcriptional regulator from Streptococcus mutans to 1.85A
Authors: Stein, A.J. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Joachimiak, A.
History
DepositionMay 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TetR/AcrR transcriptional regulator
B: TetR/AcrR transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)50,8272
Polymers50,8272
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-25 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.490, 80.197, 110.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TetR/AcrR transcriptional regulator


Mass: 25413.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU_134 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DWD0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.21 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 20% PEG 3350, 0.2M Sodium acetate, pH 8.0, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 39086 / % possible obs: 99.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Χ2: 1.847 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.926.10.59838680.96100
1.92-1.996.10.37738600.963100
1.99-2.086.10.22738420.989100
2.08-2.196.10.15238781.033100
2.19-2.336.10.10838571.157100
2.33-2.516.10.08639041.254100
2.51-2.766.10.06939101.628100
2.76-3.1660.06539292.754100
3.16-3.995.80.04939663.452100
3.99-505.60.04340724.44197.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementResolution: 1.85→33.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.469 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1957 5 %RANDOM
Rwork0.221 ---
obs0.223 39025 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.309 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3153 0 0 183 3336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223268
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.9584453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1415414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76425.302149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95515569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.715158
X-RAY DIFFRACTIONr_chiral_restr0.080.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022430
X-RAY DIFFRACTIONr_mcbond_it0.5091.52018
X-RAY DIFFRACTIONr_mcangle_it0.86923252
X-RAY DIFFRACTIONr_scbond_it1.59931250
X-RAY DIFFRACTIONr_scangle_it2.4314.51192
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 140 -
Rwork0.282 2708 -
all-2848 -
obs--99.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
113.12294.3499-5.28272.513-4.63529.9382-0.15830.8039-0.1494-0.16220.098-0.070.50870.07120.06030.49340.0138-0.13250.1961-0.00910.244151.353-2.633615.1878
28.4381-1.89769.69297.7857-1.160429.24960.16180.55080.1906-0.1324-0.3883-0.0227-0.07410.10780.22650.0888-0.0041-0.00540.2960.01340.298238.9413-2.132312.2062
37.0327-2.8543-1.30235.61430.40694.9148-0.0743-0.2498-0.01070.07720.1191-0.327-0.06170.4059-0.04480.0416-0.0576-0.00910.1940.01460.16629.45093.564912.1313
46.096-0.9432-2.41113.1183-2.65829.6404-0.0251-0.01920.16730.05870.08710.2076-0.6978-0.503-0.0620.1150.01790.00740.14760.03260.202217.85069.26078.49
519.71147.64731.34112.97270.495522.69680.1464-0.45970.90190.0309-0.1380.3251-0.99860.0197-0.00840.1604-0.1020.11490.1688-0.09710.238226.72579.74985.1872
62.86090.3265-4.50566.464-0.64867.548-0.05780.1528-0.2036-0.3913-0.01860.10210.0968-0.13210.07650.1124-0.0049-0.03840.1443-0.00960.187825.74450.18463.4522
73.02720.5891-2.61630.1678-1.343815.9174-0.0714-0.4067-0.2742-0.0112-0.1002-0.06850.15940.41180.17160.0657-0.0313-0.04050.190.0530.298120.2762-2.352420.2728
82.98671.238-3.00240.7526-1.77087.02210.0615-0.1561-0.07310.1958-0.2535-0.2344-0.02250.66910.1920.2482-0.0955-0.13870.26270.10120.302816.4799-4.378839.8034
96.82061.6608-4.40050.9769-2.09894.69840.0117-0.78980.32220.2634-0.0509-0.0497-0.40530.25930.03920.4935-0.0609-0.11030.1892-0.01240.22539.67821.557446.4644
104.34460.1856-0.18791.7051-4.05169.79750.15580.00250.110.028-0.0507-0.0305-0.08430.2312-0.10520.1935-0.1252-0.07530.1994-0.02940.310116.02686.731533.3449
1110.91929.78161.156216.5394.05791.31180.1772-0.08710.42960.1113-0.0462-0.0015-0.06660.0494-0.1310.293-0.15070.06140.19110.02510.17215.13446.775219.644
1214.6996-1.6001-0.452210.52021.54039.37650.1501-0.080.19790.19630.06780.0228-0.65820.2715-0.21790.09350.0313-0.01610.11930.00410.12947.48643.866616.287
133.57251.29661.87016.5761-1.069120.69530.03340.0696-0.2335-0.0544-0.1095-0.0748-0.069-0.00530.07610.00230.0012-0.00210.05270.01420.18079.846-3.53816.5203
146.09280.9369-7.49390.1609-1.661524.6858-0.04340.1236-0.4929-0.01370.0126-0.05720.2214-0.00640.03080.0569-0.0184-0.03080.07140.04730.19929.0406-5.367928.7732
155.34163.0651-1.40063.9743-4.524210.08690.0198-0.175-0.13280.3223-0.2113-0.39380.01290.50990.19150.16830.0017-0.06560.08750.0040.16287.0916-9.355141.3264
162.830910.83787.703242.453129.454920.963-0.0721-0.09290.04430.227-0.04080.4204-0.2219-0.25590.11290.430.0550.03760.2380.06910.20453.9318-12.417548.5716
171.18830.0660.681310.8008-2.99141.8792-0.04750.0973-0.10430.06140.0276-0.0265-0.1012-0.05970.01990.08230.0025-0.00790.1005-0.00440.10060.8046-3.623136.3596
1817.53471.9689.25845.6378-4.816511.2205-0.66560.91580.5999-0.1081-0.1705-0.4285-0.3240.78730.83610.2511-0.1018-0.07720.18340.07780.32248.485311.861631.3174
194.5825-1.2923-1.582111.13648.887313.37120.05170.37710.1296-0.825-0.0801-0.3243-0.53310.18140.02840.3157-0.0805-0.04290.33470.11670.37099.317118.623631.4907
201.71531.3069-0.96465.6699-2.61082.26620.0474-0.14640.17660.3317-0.1728-0.133-0.18020.21560.12540.2731-0.0267-0.03730.162-0.01990.12872.20267.788143.8612
2128.302-14.119518.37947.0499-9.171311.9371-0.0698-1.9073-1.54870.02741.04660.7996-0.0726-1.268-0.97670.43370.1206-0.331.2447-0.04610.5987-13.718116.4403-3.4847
228.7552-6.12167.031815.6802-7.23756.1257-0.0845-0.326-0.2201-0.20410.3670.8625-0.0019-0.3415-0.28250.1782-0.11660.04660.5521-0.29130.2647-9.50929.581-0.7158
2310.2707-1.0322-0.43979.2293.31218.26560.03710.1457-0.81480.2428-0.0560.0950.7448-0.14730.01890.1720.0236-0.01990.1886-0.00710.13420.15765.38584.218
2414.26677.3749-5.29867.2579-0.909610.70850.05460.5745-0.6217-0.503-0.0002-0.33560.6339-0.0602-0.05440.20960.05410.00420.2641-0.07290.147-0.14437.5843-5.7982
259.91285.0832-6.223614.8755-0.6139.25510.34990.58070.0235-0.6971-0.570.0856-0.5465-0.3630.22010.30250.0365-0.06790.42470.00570.1608-4.356312.0117-9.3225
269.9663-7.95531.47596.4113-2.075913.72710.81380.78630.1949-0.611-0.5893-0.1306-0.5246-0.0988-0.22450.4276-0.0354-0.05910.32230.04410.2112-2.034417.3099-3.0107
275.525-1.2431-3.06924.69843.839.69710.01260.35410.0612-0.22970.00870.1717-0.2552-0.6047-0.02120.1130.0409-0.0330.1212-0.01790.1071-5.76116.93217.7885
2814.4316-1.7642-3.21248.4647-6.018820.0316-0.61280.23690.3214-1.12050.09550.4324-0.2669-1.52420.51730.3420.0976-0.11550.2657-0.04370.273-13.142717.953616.471
295.7068-1.304-8.1491.11350.33823.433-0.16210.1428-0.2202-0.0197-0.31230.3689-0.1067-0.29310.47430.27680.03740.02210.3448-0.00370.3525-17.361318.247326.6062
3011.7697-3.51740.182817.5767-3.149612.7458-0.04580.0055-0.09710.1191-0.08340.4558-0.1248-1.01260.12920.1997-0.02840.06740.2811-0.03820.2562-18.882915.404838.3789
315.69671.0933-1.78251.90335.280219.35610.0837-0.2147-0.08680.1888-0.09150.04560.48-0.10820.00780.16240.00820.08550.19760.03310.3887-15.28687.94233.0992
323.4690.5069-3.19350.6731.718416.2197-0.08440.50680.1433-0.192-0.05570.2856-0.3795-0.61520.140.18150.033-0.03170.3070.01720.3162-12.48656.467619.8718
3313.3823.75441.62318.59830.28434.2771-0.16970.1933-0.16390.15760.04190.05840.5019-0.09810.12780.13280.0074-0.01460.08750.01320.0906-1.40157.928113.4889
349.8889-3.8456-4.37024.56522.88256.54710.06910.0885-0.05360.2946-0.004-0.5009-0.16560.3396-0.06510.09690.0077-0.04050.0713-0.02160.16693.51216.095215.1974
356.0761.4259-5.73348.0723-2.998318.98340.072-0.07510.16150.1085-0.1346-0.2516-0.20580.34360.06270.11340.0298-0.0270.0656-0.02420.1281-3.819118.388823.8697
365.2127-1.6729-4.40134.35613.04937.95450.041-0.1630.15430.3597-0.08550.482-0.056-0.25470.04450.2077-0.00230.03140.1433-0.00360.2274-11.359921.519837.9691
370.3654-0.01461.0054.15850.9333.026-0.04490.0313-0.05550.52890.279-0.01960.04120.2176-0.23410.27150.0201-0.0120.2297-0.05080.3081-4.746423.69541.5763
3831.56760.982210.30016.17225.5744-0.06360.14680.096-0.14860.0592-0.0707-0.26670.120.00440.1113-0.0012-0.00560.07420.0420.1007-3.59137.767930.3673
394.48770.3181-1.4578.7302-2.97478.5322-0.0170.123-0.6287-0.07230.0937-0.01060.8164-0.3549-0.07670.1882-0.074-0.02160.214-0.0340.2439-7.9605-8.373828.4225
401.3286-0.5613-0.1847.38914.91025.01010.0478-0.10850.05380.458-0.1720.3045-0.1219-0.27890.12420.1974-0.01360.04760.16930.02810.1568-8.91545.011140.3375
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 19
2X-RAY DIFFRACTION2A20 - 25
3X-RAY DIFFRACTION3A26 - 36
4X-RAY DIFFRACTION4A37 - 50
5X-RAY DIFFRACTION5A51 - 56
6X-RAY DIFFRACTION6A57 - 73
7X-RAY DIFFRACTION7A74 - 85
8X-RAY DIFFRACTION8A86 - 102
9X-RAY DIFFRACTION9A103 - 113
10X-RAY DIFFRACTION10A114 - 123
11X-RAY DIFFRACTION11A124 - 129
12X-RAY DIFFRACTION12A130 - 134
13X-RAY DIFFRACTION13A135 - 143
14X-RAY DIFFRACTION14A144 - 151
15X-RAY DIFFRACTION15A152 - 160
16X-RAY DIFFRACTION16A161 - 165
17X-RAY DIFFRACTION17A166 - 184
18X-RAY DIFFRACTION18A185 - 189
19X-RAY DIFFRACTION19A190 - 196
20X-RAY DIFFRACTION20A197 - 217
21X-RAY DIFFRACTION21B24 - 29
22X-RAY DIFFRACTION22B30 - 35
23X-RAY DIFFRACTION23B36 - 47
24X-RAY DIFFRACTION24B48 - 54
25X-RAY DIFFRACTION25B55 - 64
26X-RAY DIFFRACTION26B65 - 71
27X-RAY DIFFRACTION27B72 - 82
28X-RAY DIFFRACTION28B83 - 87
29X-RAY DIFFRACTION29B88 - 98
30X-RAY DIFFRACTION30B99 - 106
31X-RAY DIFFRACTION31B107 - 115
32X-RAY DIFFRACTION32B116 - 123
33X-RAY DIFFRACTION33B124 - 132
34X-RAY DIFFRACTION34B133 - 143
35X-RAY DIFFRACTION35B144 - 150
36X-RAY DIFFRACTION36B151 - 164
37X-RAY DIFFRACTION37B165 - 171
38X-RAY DIFFRACTION38B172 - 190
39X-RAY DIFFRACTION39B191 - 199
40X-RAY DIFFRACTION40B200 - 217

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