[English] 日本語
Yorodumi
- PDB-3knw: Crystal structure of a putative transcriptional regulator (TetR/A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3knw
TitleCrystal structure of a putative transcriptional regulator (TetR/AcrR family member) from putative transcriptional regulator (TetR/AcrR family)
ComponentsPutative transcriptional regulator (TetR/AcrR family)
Keywordstranscription regulator / TetR-like protein / MCSG / PSI / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


Tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / 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
Putative transcriptional regulator (TetR/AcrR family)
Similarity search - Component
Biological speciesAcinetobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsNocek, B. / Bigelow, L. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a putative transcriptional regulator (TetR/AcrR family member) from putative transcriptional regulator (TetR/AcrR family)
Authors: Nocek, B. / Bigelow, L. / Cobb, G. / Joachimiak, A.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative transcriptional regulator (TetR/AcrR family)
B: Putative transcriptional regulator (TetR/AcrR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1143
Polymers49,0522
Non-polymers621
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-25 kcal/mol
Surface area16890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.741, 73.768, 106.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsauthors state that the biological assembly is highly likely dimer

-
Components

#1: Protein Putative transcriptional regulator (TetR/AcrR family)


Mass: 24525.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. (bacteria) / Strain: ADP1 / Gene: ACIAD2740 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 magic / References: UniProt: Q6F8X8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS, 20% PEG-1000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 18, 2009 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. all: 19022 / Num. obs: 18816 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 65.8 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 23.5
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.8 / Num. unique all: 908 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
Auto-Rickshawphasing
SHELXmodel building
CCP4model building
MLPHAREphasing
NANtMRFmodel building
DMmodel building
RESOLVEmodel building
SHARPphasing
ARP/wARPmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
CCP4phasing
NANtMRFphasing
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 18.429 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.356 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26327 961 5.2 %RANDOM
Rwork0.20992 ---
all0.213 17997 --
obs0.21265 17687 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.764 Å2
Baniso -1Baniso -2Baniso -3
1--2.87 Å20 Å20 Å2
2---2.39 Å20 Å2
3---5.26 Å2
Refinement stepCycle: LAST / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 4 25 2863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222885
X-RAY DIFFRACTIONr_bond_other_d0.0010.021960
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9713880
X-RAY DIFFRACTIONr_angle_other_deg0.99234800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3465355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90724.333120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.5915546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1521513
X-RAY DIFFRACTIONr_chiral_restr0.0940.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023128
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8641.51775
X-RAY DIFFRACTIONr_mcbond_other0.1871.5732
X-RAY DIFFRACTIONr_mcangle_it1.58122838
X-RAY DIFFRACTIONr_scbond_it2.28831110
X-RAY DIFFRACTIONr_scangle_it3.564.51042
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 68 -
Rwork0.262 1262 -
obs--96.94 %
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)
10.30762.1052-0.006615.12553.577226.61390.03-0.0224-0.0666-0.0286-0.1891-0.7685-1.0836-0.93510.15910.4139-0.0865-0.09060.323-0.01940.578355.836458.220335.0018
21.2898-4.5035-1.806317.601212.475923.93760.29050.0730.5775-0.90830.4548-1.9514-0.57621.9001-0.74530.4711-0.05320.08830.69770.02360.37158.808950.483525.0211
34.32170.22545.20376.61424.923111.5960.3830.3603-0.14210.5138-0.2329-0.09461.3960.1911-0.15010.58270.0251-0.06470.3247-0.00750.238456.389443.914231.8509
410.95676.42098.340221.37.921116.2960.2843-0.91550.46460.1292-0.66260.3786-0.2351-0.98790.37830.3458-0.04460.05530.41070.04060.132348.424348.936535.5434
53.3232-3.92440.121815.8384-11.314211.2720.0231-0.12620.25840.25230.06970.0042-0.23060.085-0.09280.3591-0.06840.01160.3803-0.01310.350249.316354.860624.8878
66.228-4.2669-7.16079.86363.709647.5573-0.3845-0.08630.35491.3041-0.02-0.4326-1.02220.13090.40460.4112-0.1204-0.01820.33790.01460.431552.166164.356419.4293
75.4091-1.4972-2.700415.3078-3.59712.68540.5276-0.09840.04590.4686-0.52460.0666-0.66310.3071-0.0030.8532-0.2125-0.03740.4331-0.04020.666655.378972.655513.1687
84.2513-1.6239-0.979317.36522.50211.7152-0.0090.12340.62850.2434-0.0327-0.1634-0.46920.58180.04180.477-0.1073-0.0340.39880.0480.546656.948672.20983.1414
97.4208-4.18724.089518.77227.117.6658-0.2734-0.04811.16390.38580.1525-1.52790.02490.0980.12090.3125-0.0166-0.01510.4804-0.06450.529459.70864.81257.1154
101.35624.3859-1.161915.6617-4.43151.31050.5159-0.45010.19510.6725-0.56890.41170.00630.07010.0530.8994-0.13910.13871.0009-0.12410.694161.412657.621310.2855
1124.97722.3158-7.16120.2286-0.45936.02250.2310.2720.50920.08060.05640.04260.6846-0.1878-0.28750.5939-0.0032-0.05930.40.03890.065248.182245.085215.9341
120.7958-2.4375-1.280714.8015-8.188722.12790.02990.1021-0.05230.31410.19820.4108-0.3171-1.0106-0.22810.3644-0.04430.05780.54880.02190.378641.396750.776119.4052
136.92847.0262-6.83810.3388-1.79223.05170.2131-0.19320.16750.34920.10150.36180.5051-0.6706-0.31450.3523-0.03690.03050.51040.05620.429143.45756.03413.3099
145.27762.5131-0.08699.9906-0.19183.6417-0.1461-0.18610.45990.73420.53760.2119-0.2249-0.5031-0.39160.19880.01350.03920.18820.0030.416446.496767.54826.7175
1510.179810.9439-3.472222.31273.08345.81670.22950.24140.0509-0.4205-0.1951-0.038-0.6237-0.1088-0.03450.3142-0.0228-0.03470.32760.08890.416449.727974.1164-4.1283
165.30721.9616-1.66734.2255-0.81933.03850.0410.05160.342-0.15240.15210.15480.14360.0331-0.19310.1599-0.0223-0.00010.2060.00860.329446.74361.9523-0.41
177.6998-4.73214.61886.8568-0.87893.74970.0281-0.1671-0.1117-0.07440.03160.0838-0.0135-0.093-0.05980.1687-0.0340.03010.26840.04080.254255.988852.62822.8627
189.892.9831-1.642912.072-1.484810.23480.3072-0.6503-0.32160.5352-0.1983-0.11160.2535-0.1457-0.10890.1696-0.0241-0.04090.24690.01780.285565.578147.71084.5123
1910.8969-6.69182.45994.8645-0.71531.39430.10190.48050.3512-0.1939-0.119-0.2579-0.10210.31510.01710.2083-0.0370.01390.30720.04990.394362.862857.9556-1.4739
2019.2628-4.5878-4.724525.1028-6.455419.77220.17280.80280.6633-1.2030.0898-0.45960.27170.5852-0.26260.2815-0.05650.06680.22510.080.324956.685965.5938-6.1107
2110.51933.097410.035510.70645.425810.20050.29580.6002-0.2526-1.0695-0.35581.31290.05140.4320.060.6122-0.0614-0.0720.4057-0.02850.727553.256817.19263.2707
2212.4824-5.4871-4.875417.3466.195118.91-0.2091.0216-0.06690.4763-0.2081.139-0.7549-1.52880.4170.36770.0118-0.05070.19180.06420.420252.038328.86248.7213
2360.361921.635310.500912.849711.178312.62960.4717-1.632-1.98270.4643-0.9643-0.00240.3712-0.66360.49260.70730.07580.29140.40040.50440.870353.578922.551615.6524
2419.3399-5.4879-1.600512.40161.170526.29720.1489-0.2776-1.4626-0.4304-0.4670.39181.58350.12950.31810.42310.0787-0.02030.21630.05340.456660.25315.19669.5541
254.9794-4.64854.75678.3081-9.389115.7040.12020.31-0.1284-0.2077-0.4383-0.49190.76730.22220.3180.33560.0164-0.11210.1688-0.04860.541960.406226.85113.2056
265.8917-5.21026.136212.15321.574112.91080.4370.26270.0428-0.2963-0.4086-0.18520.59250.0435-0.02840.3305-0.0642-0.0120.3179-0.11620.392152.058134.4588-11.6414
274.3401-1.37490.86964.2749-6.562711.44240.25080.44720.2059-0.8338-0.37290.04381.7648-0.46830.12210.8208-0.2591-0.11961.016-0.20420.420447.604242.451-21.5998
282.7873-4.134-1.221611.16622.2337.5161-0.04430.4973-0.0563-0.7668-0.12490.17120.1581-0.51310.16920.3684-0.048-0.06260.4249-0.01820.32247.202844.2753-13.3709
2923.5089-4.368812.899911.43479.239234.3486-0.18250.2822-0.23750.5472-0.28480.51740.25-0.09950.46730.4603-0.05050.00550.3033-0.03180.381544.557442.3367-4.5151
305.9915-9.8062-7.951816.203113.065310.5709-0.06020.17490.10580.42390.0735-0.03740.2746-0.1483-0.01330.5640.13750.03510.55090.21170.476454.642140.02497.1178
318.86645.6725-2.997323.376210.103315.22560.5446-0.014-0.73450.8421-0.2636-0.7832-0.1252-0.0164-0.28110.33860.0473-0.16370.16890.15360.351565.277736.72118.8141
3215.1447-5.64365.61487.4665-5.962814.520.51050.13520.1808-0.0067-0.4297-0.69350.35590.6662-0.08080.32870.0179-0.05050.3528-0.07980.443664.21738.9669-1.6904
3312.14272.2143-7.14390.4131-1.31614.2254-0.12150.1212-0.127-0.09230.0447-0.03350.1879-0.05320.07680.52060.038-0.02360.4516-0.09480.412258.967742.4294-10.6245
340.9965.4022-0.95430.8183-1.144711.9893-0.23550.0025-0.3374-0.7736-0.0603-1.83230.78530.20460.29580.422-0.02440.03170.6409-0.04860.171456.922847.4178-19.2453
3512.00083.43258.44537.18024.982721.94760.32980.78870.6915-1.2142-0.2002-0.1215-0.10510.4352-0.12960.45-0.06530.0960.4270.09010.205855.649853.9983-18.9226
362.8976-1.48580.62915.20914.13924.6147-0.08710.37080.1172-0.00970.1128-0.119-0.09460.3803-0.02570.223-0.01720.01690.38960.02060.29755.373851.1452-5.8647
379.26240.3882-2.57633.63190.70320.9150.079-0.4568-0.3034-0.2003-0.0709-0.1751-0.12030.1355-0.00810.2448-0.03110.0220.25320.00570.321848.88948.72732.049
387.9437-2.1521.024617.37915.551221.69320.1441-0.451-0.47720.13540.1739-0.18290.2888-0.3246-0.31810.1838-0.0367-0.0390.34880.05960.262741.407747.58017.5194
396.86880.6247-2.61682.51512.92485.0748-0.1620.29750.0526-0.11250.04230.1038-0.0161-0.11670.11970.26950.00780.01510.29250.02390.297542.474652.4145-4.2119
4019.0101-0.63991.750722.90872.376535.87930.0670.84841.2303-1.1097-0.39330.1674-1.5182-0.35970.32630.34470.0575-0.02970.40710.07730.286346.986256.8571-13.4012
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 15
2X-RAY DIFFRACTION2A16 - 26
3X-RAY DIFFRACTION3A27 - 47
4X-RAY DIFFRACTION4A48 - 56
5X-RAY DIFFRACTION5A57 - 67
6X-RAY DIFFRACTION6A68 - 72
7X-RAY DIFFRACTION7A73 - 81
8X-RAY DIFFRACTION8A82 - 89
9X-RAY DIFFRACTION9A90 - 94
10X-RAY DIFFRACTION10A95 - 109
11X-RAY DIFFRACTION11A110 - 123
12X-RAY DIFFRACTION12A124 - 128
13X-RAY DIFFRACTION13A129 - 134
14X-RAY DIFFRACTION14A135 - 146
15X-RAY DIFFRACTION15A147 - 156
16X-RAY DIFFRACTION16A157 - 167
17X-RAY DIFFRACTION17A168 - 176
18X-RAY DIFFRACTION18A177 - 184
19X-RAY DIFFRACTION19A185 - 192
20X-RAY DIFFRACTION20A193 - 198
21X-RAY DIFFRACTION21B12 - 16
22X-RAY DIFFRACTION22B17 - 30
23X-RAY DIFFRACTION23B31 - 40
24X-RAY DIFFRACTION24B46 - 52
25X-RAY DIFFRACTION25B53 - 68
26X-RAY DIFFRACTION26B69 - 78
27X-RAY DIFFRACTION27B79 - 85
28X-RAY DIFFRACTION28B86 - 92
29X-RAY DIFFRACTION29B93 - 108
30X-RAY DIFFRACTION30B109 - 116
31X-RAY DIFFRACTION31B117 - 126
32X-RAY DIFFRACTION32B127 - 134
33X-RAY DIFFRACTION33B135 - 141
34X-RAY DIFFRACTION34B142 - 147
35X-RAY DIFFRACTION35B148 - 161
36X-RAY DIFFRACTION36B162 - 169
37X-RAY DIFFRACTION37B170 - 176
38X-RAY DIFFRACTION38B177 - 183
39X-RAY DIFFRACTION39B184 - 193
40X-RAY DIFFRACTION40B194 - 198

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more