[English] 日本語
Yorodumi
- PDB-3him: The Crystal Structure of a Bacterial Regulatory Protein in the te... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3him
TitleThe Crystal Structure of a Bacterial Regulatory Protein in the tetR Family from Rhodococcus RHA1 to 2.2A
ComponentsProbable transcriptional regulator
KeywordsTRANSCRIPTION REGULATOR / TetR / Bacterial / Rhodococcus / RHA1 / PSI-2 / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


HTH-type transcriptional repressor KstR2, C-terminal / 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
Probable transcriptional regulator
Similarity search - Component
Biological speciesRhodococcus jostii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsStein, A.J. / Binkowski, T.A. / Evdokimova, E. / Kagan, O. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of a Bacterial Regulatory Protein in the tetR Family from Rhodococcus RHA1 to 2.2A
Authors: Stein, A.J. / Binkowski, T.A. / Evdokimova, E. / Kagan, O. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionMay 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable transcriptional regulator
B: Probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)45,3572
Polymers45,3572
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-14 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.053, 63.042, 94.766
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Probable transcriptional regulator


Mass: 22678.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii (bacteria) / Strain: RHA1 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0SD48
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 30% PEG 4000, 0.2M Ammonium acetate, 0.1M Sodium citrate pH 5.6, vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2006
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 22502 / % possible obs: 98.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.082 / Χ2: 0.775 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.184.20.34619560.6186.7
2.18-2.264.70.28522350.5511100
2.26-2.374.70.22622560.5621100
2.37-2.494.70.18422520.521199.9
2.49-2.654.70.15322660.523199.9
2.65-2.854.70.11422640.555199.8
2.85-3.144.70.08922650.639199.8
3.14-3.594.60.0723070.821100
3.59-4.524.50.05723181.156199.1
4.52-504.20.0623831.881197.1

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0054refinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000phasing
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementResolution: 2.2→28.1 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.195 / SU B: 12.64 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 998 5.2 %RANDOM
Rwork0.197 ---
obs0.2 19271 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.379 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2831 0 0 132 2963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212915
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.9383994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7275388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19721.636110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04915406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2991522
X-RAY DIFFRACTIONr_chiral_restr0.0810.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212220
X-RAY DIFFRACTIONr_mcbond_it0.4771.51917
X-RAY DIFFRACTIONr_mcangle_it0.85823061
X-RAY DIFFRACTIONr_scbond_it1.5543998
X-RAY DIFFRACTIONr_scangle_it2.4514.5929
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2570.306700.2331319139199.856
2.257-2.3180.259710.221306138199.71
2.318-2.3850.272820.191234131899.848
2.385-2.4580.217690.191244131899.621
2.458-2.5380.273690.21172124899.439
2.538-2.6260.295590.2021168123399.513
2.626-2.7240.28560.1881110117699.15
2.724-2.8340.229540.2061071113499.206
2.834-2.9590.259710.2241017109699.27
2.959-3.1020.247590.237982105199.049
3.102-3.2670.25490.219958101399.408
3.267-3.4630.307550.21888494599.365
3.463-3.6980.258450.19385190399.225
3.698-3.9880.251450.1777983398.92
3.988-4.360.146330.1673578198.335
4.36-4.860.191370.16166471797.768
4.86-5.5840.35270.20857964094.688
5.584-6.7730.343190.23251554897.445
6.773-9.3120.189180.16341744398.194
9.312-28.1050.118100.20226829394.881
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)
16.36452.05020.11762.09112.15697.5640.15380.0185-0.8044-0.0814-0.1767-0.08250.6520.45460.02290.28410.0562-0.05220.2502-0.05360.1955.0987-31.675-18.3042
22.9671-2.1772-1.16826.37954.37214.68960.00520.19250.3449-0.2195-0.1790.1246-0.4238-0.04630.17380.1852-0.03370.00580.15920.00490.17212.5043-20.3852-17.0516
31.5110.9555-0.18673.60142.2771.97690.1476-0.0740.1929-0.0066-0.2230.1873-0.1864-0.16330.07540.2710.0163-0.00540.2116-0.02370.2731-3.0897-15.8096-12.1569
44.3298-0.30960.03611.51481.93626.87530.026-0.1820.0932-0.0405-0.02060.1557-0.0841-0.5263-0.00540.16440.0016-0.00970.1967-0.01580.1867-6.5427-26.9039-16.7071
52.5930.5432-0.15521.13820.56532.9002-0.0383-0.1524-0.0902-0.0822-0.068-0.0187-0.0772-0.05740.10620.1704-0.01070.01390.1630.01450.15110.1194-27.6764-7.0662
67.46012.239-1.63130.8333-0.52240.36610.0152-0.139-0.19180.0248-0.0625-0.09540.01510.04020.04730.2027-0.0007-0.01140.14240.00040.148511.2262-21.5365-10.4545
72.50142.0984-0.5372.2223-0.22681.7958-0.0332-0.1392-0.1451-0.04020.0448-0.28530.18790.3461-0.01160.17540.04910.0120.1697-0.00410.172232.3764-16.32-17.2907
85.58850.2698-0.34860.96410.17911.3990.0152-0.0439-0.136-0.07690.0296-0.00540.089-0.0609-0.04490.16240.00570.01050.09910.00670.130523.679-11.7609-19.9503
97.27670.9818-3.88613.78043.427711.39530.08870.23540.3323-0.04090.05930.1086-0.5206-0.2594-0.1480.1685-0.0023-0.00430.1623-0.00480.18969.0496-12.5463-17.8499
100.52930.7226-0.25756.6282-3.44783.2695-0.066-0.1554-0.10630.1156-0.0184-0.0680.04920.08560.08440.2041-0.00260.00480.20820.00110.19949.265-11.2312-9.2008
113.5079-0.5690.36630.41990.18440.6720.2055-0.4627-0.06290.1137-0.122-0.0382-0.02470.0211-0.08340.3167-0.1027-0.0020.31390.01160.194112.9282-17.564-1.8634
122.71230.3136-1.38660.23590.86976.07590.1657-0.2783-0.13440.1133-0.0977-0.0360.38980.003-0.06810.2375-0.0420.00990.2155-0.00060.196926.8121-13.4722-9.5456
133.5007-3.2872-0.18677.53742.57982.6236-0.0274-0.2517-0.23910.21830.024-0.18090.12220.50750.00330.20640.0112-0.01560.35580.05420.226134.9166-10.1918-8.9233
142.5897-3.6454-2.46376.3162.46263.3736-0.157-0.31940.16310.26120.1961-0.5850.15990.6628-0.03910.2210.0002-0.04390.3881-0.07460.319841.2214-4.5384-11.1559
157.5415-1.86312.13260.4876-0.94857.1649-0.03890.26820.29360.0403-0.0697-0.0763-0.39490.21950.10860.1642-0.0202-0.00150.16260.00320.191732.0365-1.2737-5.0819
160.8691-0.0687-0.55130.00590.04480.3820.0308-0.13970.2140.00110.0287-0.0115-0.04240.0792-0.05950.16760.012-0.01090.1278-0.0180.204722.101-5.646-11.424
172.2713-1.52840.95291.5146-0.41994.82860.05110.22050.2425-0.102-0.0435-0.0206-0.16380.0086-0.00760.1420.0071-0.01390.14560.00940.164813.518-2.1073-22.9617
186.9574.02223.32173.2088-0.48298.1321-0.19780.347-0.1771-0.21340.2224-0.13370.18690.0818-0.02460.17460.0188-0.0010.1657-0.00490.16221.289-5.4711-28.0945
194.46380.7721-0.10050.87950.94792.1242-0.0044-0.03930.02620.0134-0.0149-0.0289-0.22420.2290.01930.1403-0.01770.01020.1169-0.00520.109727.5035-0.7615-21.4179
206.64852.0685-1.00553.825-2.05346.34610.31340.22950.0361-0.4976-0.3036-0.6009-0.11340.925-0.00970.2679-0.0240.05540.3018-0.01050.249235.02581.5401-16.4345
216.6888-1.35-0.84860.27890.34215.9704-0.00230.19950.5118-0.0381-0.0225-0.1198-0.71910.58640.02490.3979-0.05350.12050.2936-0.0650.3773-8.020813.5809-2.8419
223.7564-4.319-3.26375.38862.56746.1795-0.1285-0.1195-0.0270.17320.01130.00050.03230.37480.11730.1308-0.0229-0.00430.2408-0.03930.1946-6.08013.9393-0.795
231.8929-0.8960.012.99784.28497.160.0385-0.1043-0.1950.35630.08280.01020.66940.0896-0.12130.29770.0110.05390.26240.01560.2874-5.1417-6.0651-6.4483
240.92551.61550.53715.33051.72830.56330.1465-0.0438-0.23630.3585-0.20620.1540.1261-0.0960.05970.3135-0.03990.01270.35480.01010.327-12.431-4.3243-3.9752
257.42961.884-0.64943.0330.90883.7176-0.1195-0.0255-0.02370.0470.05530.39490.2018-0.40210.06420.2705-0.01170.00770.2594-0.01250.2521-14.0291-0.10454.0397
262.2707-2.624-1.30428.2461-2.30213.5601-0.16810.1456-0.1084-0.31110.16020.25530.5568-0.37310.00780.3746-0.0671-0.00250.4037-0.02050.2981-19.00513.2377-3.539
272.5119-0.1052-2.41423.10141.9144.0635-0.05420.07810.24590.29380.17150.34890.0065-0.242-0.11730.19280.03020.00770.23230.01520.2186-13.00815.0281-9.3165
287.36442.13450.14314.0179-0.11790.10520.1107-0.09310.1483-0.0083-0.10080.09380.0155-0.0412-0.00980.15630.00350.01610.1471-0.01770.1187-3.92426.6787-10.504
295.19054.6599-0.46846.11930.50691.48490.0376-0.12980.31840.1103-0.02150.1116-0.1538-0.0642-0.01610.14960.02-0.00570.1033-0.00940.14419.978114.7246-9.6498
306.77871.3446-2.00770.39180.40025.76020.13420.00130.4353-0.02480.00440.0864-0.30830.1233-0.13860.2038-0.0426-0.01130.1334-0.00860.198923.959821.715-9.9455
312.86361.9148-1.17162.4519-1.30591.6539-0.0428-0.08380.06780.10220.07220.088-0.0158-0.1036-0.02940.13290.0138-0.00720.1073-0.02090.123614.65238.4946-5.6191
326.93281.74321.26445.73974.24517.90970.23550.0747-0.1633-0.2001-0.0339-0.15660.3680.2047-0.20160.1754-0.00730.0010.15850.02070.17984.0456-1.3511-9.2404
333.2358-0.6766-0.83142.1817-1.49512.2749-0.1147-0.1448-0.1612-0.01390.0993-0.10630.3844-0.00230.01540.19570.0132-0.00420.2099-0.01760.1571-2.78952.8317-18.9961
346.34553.02850.09221.46850.07420.3449-0.06760.1760.1220.02250.05930.0586-0.0308-0.030.00830.1849-0.00010.00480.1653-0.00110.16027.928810.8075-18.4518
350.83040.1837-0.43281.5116-0.9312.13510.0120.16520.0104-0.1099-0.036-0.0762-0.09430.03360.0240.1618-0.0216-0.0030.1253-0.01780.148526.182514.3523-19.4914
362.28160.9218-2.02511.8081-2.0692.8922-0.01190.16270.02230.01010.012-0.0394-0.0263-0.1064-0.00020.1671-0.0267-0.00430.1287-0.02310.168318.06583.6529-15.4458
372.18690.93951.46010.71160.90111.41590.037-0.3847-0.2180.1448-0.0445-0.10210.1474-0.0810.00750.2070.0090.00850.20540.04020.192216.8667-2.9563-0.101
384.89791.43280.15385.9674-0.96129.9333-0.0449-0.41060.17370.28440.0947-0.0743-0.10260.1677-0.04980.15690.0013-0.01450.1460.00230.164623.00734.6710.1209
391.15981.6846-0.3297.5639-2.43385.0617-0.1930.07620.05150.03560.10940.1064-0.08720.14860.08360.1623-0.0149-0.01190.1383-0.00610.151826.52185.8108-8.2941
401.5508-1.3451-2.37118.5328-1.4255.3519-0.0758-0.24730.26090.56050.0282-0.8716-0.19350.42110.04760.22850.0203-0.1270.2053-0.04740.411832.25818.4133-13.194
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 20
2X-RAY DIFFRACTION2A21 - 29
3X-RAY DIFFRACTION3A30 - 40
4X-RAY DIFFRACTION4A41 - 53
5X-RAY DIFFRACTION5A54 - 61
6X-RAY DIFFRACTION6A62 - 74
7X-RAY DIFFRACTION7A75 - 91
8X-RAY DIFFRACTION8A92 - 107
9X-RAY DIFFRACTION9A108 - 113
10X-RAY DIFFRACTION10A114 - 118
11X-RAY DIFFRACTION11A119 - 134
12X-RAY DIFFRACTION12A135 - 140
13X-RAY DIFFRACTION13A141 - 146
14X-RAY DIFFRACTION14A147 - 154
15X-RAY DIFFRACTION15A155 - 160
16X-RAY DIFFRACTION16A161 - 170
17X-RAY DIFFRACTION17A171 - 181
18X-RAY DIFFRACTION18A182 - 189
19X-RAY DIFFRACTION19A190 - 196
20X-RAY DIFFRACTION20A197 - 203
21X-RAY DIFFRACTION21B12 - 18
22X-RAY DIFFRACTION22B19 - 27
23X-RAY DIFFRACTION23B28 - 36
24X-RAY DIFFRACTION24B37 - 42
25X-RAY DIFFRACTION25B43 - 48
26X-RAY DIFFRACTION26B49 - 54
27X-RAY DIFFRACTION27B55 - 61
28X-RAY DIFFRACTION28B62 - 71
29X-RAY DIFFRACTION29B72 - 83
30X-RAY DIFFRACTION30B84 - 91
31X-RAY DIFFRACTION31B92 - 110
32X-RAY DIFFRACTION32B111 - 116
33X-RAY DIFFRACTION33B117 - 128
34X-RAY DIFFRACTION34B129 - 138
35X-RAY DIFFRACTION35B139 - 157
36X-RAY DIFFRACTION36B158 - 172
37X-RAY DIFFRACTION37B173 - 184
38X-RAY DIFFRACTION38B185 - 190
39X-RAY DIFFRACTION39B191 - 196
40X-RAY DIFFRACTION40B197 - 203

+
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