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- PDB-5vlg: Crystal structure of EilR in complex with malachite green -

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Basic information

Entry
Database: PDB / ID: 5vlg
TitleCrystal structure of EilR in complex with malachite green
ComponentsRegulatory protein TetR
KeywordsTRANSCRIPTION / transcription factor
Function / homology
Function and homology information


regulation of biosynthetic process / regulation of primary metabolic process / DNA binding
Similarity search - Function
Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
MALACHITE GREEN / EilR repressor
Similarity search - Component
Biological speciesEnterobacter lignolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.932 Å
AuthorsPereira, J.H. / Ruegg, T.L. / Chen, J. / Novichkov, P. / DeGiovani, A. / Tomaleri, G.P. / Singer, S. / Simmons, B. / Thelen, M. / Adams, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
CitationJournal: Nat Commun / Year: 2018
Title: Jungle Express is a versatile repressor system for tight transcriptional control.
Authors: Ruegg, T.L. / Pereira, J.H. / Chen, J.C. / DeGiovanni, A. / Novichkov, P. / Mutalik, V.K. / Tomaleri, G.P. / Singer, S.W. / Hillson, N.J. / Simmons, B.A. / Adams, P.D. / Thelen, M.P.
History
DepositionApr 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein TetR
B: Regulatory protein TetR
C: Regulatory protein TetR
D: Regulatory protein TetR
E: Regulatory protein TetR
F: Regulatory protein TetR
G: Regulatory protein TetR
H: Regulatory protein TetR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,31416
Polymers173,6788
Non-polymers2,6368
Water30617
1
A: Regulatory protein TetR
B: Regulatory protein TetR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0784
Polymers43,4202
Non-polymers6592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-11 kcal/mol
Surface area17410 Å2
MethodPISA
2
C: Regulatory protein TetR
D: Regulatory protein TetR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0784
Polymers43,4202
Non-polymers6592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-11 kcal/mol
Surface area17250 Å2
MethodPISA
3
E: Regulatory protein TetR
F: Regulatory protein TetR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0784
Polymers43,4202
Non-polymers6592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-11 kcal/mol
Surface area17370 Å2
MethodPISA
4
G: Regulatory protein TetR
H: Regulatory protein TetR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0784
Polymers43,4202
Non-polymers6592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-12 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.145, 85.985, 102.275
Angle α, β, γ (deg.)90.00, 101.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Regulatory protein TetR


Mass: 21709.783 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter lignolyticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: E3G817
#2: Chemical
ChemComp-MGR / MALACHITE GREEN


Mass: 329.458 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C23H25N2 / Comment: Antimicrobial*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Tri-Sodium citrate, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: AREA DETECTOR / Date: Oct 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.93→50.076 Å / Num. obs: 36135 / % possible obs: 99.9 % / Redundancy: 2.9 % / Net I/σ(I): 6.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2650: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementResolution: 2.932→50.076 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.79
RfactorNum. reflection% reflection
Rfree0.2401 2007 5.55 %
Rwork0.1966 --
obs0.199 36135 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.932→50.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11976 0 200 17 12193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212409
X-RAY DIFFRACTIONf_angle_d0.46816763
X-RAY DIFFRACTIONf_dihedral_angle_d9.6617299
X-RAY DIFFRACTIONf_chiral_restr0.0331825
X-RAY DIFFRACTIONf_plane_restr0.0022175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9317-3.0050.30731200.29441925X-RAY DIFFRACTION79
3.005-3.08620.35731450.2862443X-RAY DIFFRACTION100
3.0862-3.1770.3221410.27542461X-RAY DIFFRACTION100
3.177-3.27960.27461400.26062464X-RAY DIFFRACTION100
3.2796-3.39670.27331480.24582435X-RAY DIFFRACTION100
3.3967-3.53270.29581450.21852481X-RAY DIFFRACTION100
3.5327-3.69340.21431410.2032468X-RAY DIFFRACTION100
3.6934-3.88810.25641570.22477X-RAY DIFFRACTION100
3.8881-4.13160.23481410.18032472X-RAY DIFFRACTION100
4.1316-4.45040.20621410.16252475X-RAY DIFFRACTION100
4.4504-4.89790.21851480.15992479X-RAY DIFFRACTION100
4.8979-5.60590.231460.17192491X-RAY DIFFRACTION100
5.6059-7.05970.22341440.19382507X-RAY DIFFRACTION100
7.0597-50.08340.17961500.15222550X-RAY DIFFRACTION99
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)
14.40190.6274-1.53792.5799-1.55478.0357-0.06460.43880.3358-0.37210.02180.0007-0.14240.32850.06350.66980.03370.06790.44360.0580.3196-22.262130.9322-56.7171
24.5110.5428-0.54862.0572-0.64523.4336-0.13990.76340.3885-0.56050.21340.2574-0.0434-0.3372-0.04580.6867-0.0037-0.01620.47970.12750.3021-41.301726.9232-48.8885
35.57750.35831.15596.9311-5.46278.8720.0327-0.1266-0.197-0.4985-0.2696-0.31070.6230.34850.15190.33-0.0162-0.00560.30740.0240.215-23.966415.1264-12.6633
45.6328-0.90860.52983.31641.94963.8013-0.2222-0.1816-0.32380.54260.2871-0.0507-0.14330.6694-0.03210.4085-0.03230.05730.41620.00460.1881-15.848117.1403-15.2937
59.04310.07441.52410.2092-0.67082.93640.3183-0.4551-0.271-0.3119-0.1284-0.1116-0.1167-0.6957-0.19390.39450.01110.01990.23530.0390.2893-39.661319.677-23.4241
61.4306-0.8734-0.9963.0008-0.17114.53040.4461-0.15420.1579-0.6336-0.35640.064-1.58250.44570.03940.63040.03440.01020.14580.05830.4077-28.944724.8762-28.3027
78.35710.50263.60541.79960.6652.48820.4878-0.3949-0.931-0.0121-0.08170.12270.429-0.2091-0.39850.4462-0.00860.0280.34130.01180.2659-39.264713.713-30.9632
85.1521.57460.93244.87031.74364.7962-0.12330.3985-0.0843-0.97350.51160.3699-0.1344-0.4411-0.37490.5702-0.0261-0.07080.40680.1190.3132-44.719220.928-37.8645
99.20693.97991.12876.16091.6663.2678-0.18310.47790.90970.02980.4137-0.1074-1.2241-0.5631-0.20570.74910.21820.01710.43320.12920.4542-47.371630.6626-37.444
103.66154.0452.76415.79544.48494.97710.1738-0.0743-0.4646-0.39840.1605-0.22990.584-0.3036-0.33950.64540.0381-0.12060.29480.03630.4206-55.39196.2748-16.6391
116.13922.3292-1.22299.35860.48922.3263-0.03970.65640.4725-0.4145-0.34790.6538-0.7352-0.5680.28060.55150.06290.0830.2807-0.07990.4247-37.768325.9076-7.0962
126.1151.06340.1641.1405-0.83532.9863-0.0062-0.0035-0.3741-0.32490.0926-0.20480.21330.1139-0.03950.49820.13170.0130.1701-0.08370.3985-45.456813.1843-2.7067
132.9485-0.5526-0.67275.1887-0.54994.37320.2476-0.52250.4199-0.5260.0553-0.1464-0.59520.1924-0.3270.38010.0794-0.02690.252-0.06170.3082-40.568224.34156.2216
142.3272-0.7877-0.85763.43150.53035.34660.7738-0.9628-0.12440.6101-0.36421.79610.2003-1.4239-0.29970.6331-0.2910.20861.22390.2671.0503-70.47486.265728.3929
159.62190.1583-1.11622.1902-1.4558.4095-0.48830.11060.79570.1995-0.26371.114-0.7076-1.15680.47070.36710.23690.27161.88980.41921.7755-78.127711.683825.5684
161.61160.83022.19728.57112.71613.66110.108-0.3669-0.47050.40140.34260.6993-0.0023-1.2272-0.24840.27570.05030.05490.73410.15730.4844-60.851514.378824.8375
175.39174.39381.93579.61970.42695.84190.205-0.5466-0.32840.78760.0236-0.1166-0.2730.5408-0.17190.4770.1404-0.09680.6019-0.06470.3626-41.440718.931728.987
183.10252.51771.17856.050.44241.97250.0744-0.77350.12030.2619-0.01360.32770.0274-0.4719-0.02570.29250.14640.00210.5213-0.01050.2585-51.613519.877119.6271
193.9263.56231.75217.83561.0563.8223-0.0745-0.462-0.3284-0.05250.1371-0.22510.05610.1686-0.13060.24580.12790.04950.35010.02940.242-40.029617.116414.4022
203.75940.2335-2.38465.9828-2.21418.06240.00310.91140.2138-0.15280.45890.4376-0.38930.3313-0.42180.3095-0.0964-0.03290.64180.12040.294432.180646.4256-36.0534
215.15950.41631.41073.4384-0.56655.04580.01011.03790.64040.25870.2570.2326-0.61490.3016-0.29470.413-0.08160.03480.4930.16820.328628.458249.6309-32.7205
222.34553.1831-1.68592.0035-2.01571.22650.2367-0.2296-0.0018-0.1906-0.5779-1.2276-0.2099-0.07460.48380.6019-0.1430.10781.24640.28210.45373.664743.7755-41.9298
237.98430.5110.05672.24221.19962.9047-0.02741.12570.9134-0.07950.10590.3564-0.126-0.1925-0.07770.3337-0.0999-0.0140.39450.2120.4669.073844.5988-28.6945
244.57540.45390.32150.15740.73114.45830.09810.5840.3595-0.29610.18620.160.1382-0.1352-0.2680.3188-0.12590.05830.30170.13260.40672.818936.2552-23.4733
257.5416-0.2649-0.12473.6871-4.0924.5686-0.3671-0.5902-1.13930.60531.10480.38540.02280.2337-0.45410.8090.06790.060.47520.03250.371520.328129.165612.0551
267.5849-0.19040.58495.9313-1.36157.8052-0.201-0.4973-0.43680.12460.0654-0.3340.48470.77530.14790.52290.0318-0.00190.2792-0.08470.330421.641630.50084.7251
276.05392.25690.44897.8839-1.55528.6197-0.2474-1.5922-0.43250.2947-0.89130.46970.0537-0.42050.81760.6446-0.01280.28690.6067-0.06650.5538-4.816138.1366-1.673
284.88930.67831.4461.23580.43784.1370.0897-0.20810.52890.232-0.08320.20160.0101-0.2341-0.04760.5095-0.03060.08570.1362-0.04640.41344.071637.0112-10.7053
298.5731.0681.73614.11592.98158.8961-0.2980.8478-0.5082-0.5070.44560.67190.95531.1046-0.15010.72490.1698-0.10190.37030.05860.3765-13.975955.07195.5991
300.4874-1.2584-0.50135.3386-1.21125.21930.78410.3679-0.7011-1.45020.01230.95531.0637-0.6774-0.66860.633-0.0026-0.17390.4228-0.05210.4207-15.140252.6138.2966
317.9869-3.2681-3.22548.06482.87329.5752-0.24911.29470.0445-0.52130.2132-0.46180.53580.0960.10360.2248-0.03660.09440.4757-0.02860.324110.694245.106816.7562
325.06584.6272-4.89335.3627-4.59196.270.75530.2817-0.35130.5591-0.61550.0242-0.2473-0.0257-0.07810.3179-0.03230.0190.2526-0.02240.3278-7.920153.81921.3398
333.1759-0.80731.11713.52840.04382.2460.5913-0.1682-0.3131-0.7946-0.08860.2170.854-0.1964-0.29730.31120.018-0.00990.2484-0.00360.260.690337.561120.6767
344.00720.38840.59115.3157-1.06022.4215-0.0090.09020.22740.09410.1917-0.2357-0.21910.34-0.20080.2963-0.00780.02950.2832-0.03180.15175.915946.895930.3628
354.9567-4.6688-4.07285.09024.123.5308-0.9449-1.36760.39450.49711.37960.30180.50740.7182-0.06450.5264-0.04290.04141.14690.01160.6125-22.760656.605356.2001
367.15913.2044-7.15232.6326-2.20238.4530.15710.2357-0.1315-0.11980.01030.57820.1664-1.3624-0.11520.33740.02230.07260.5456-0.11510.5682-28.11355.563446.5547
377.55383.7746-3.68842.5472-2.33346.64120.2975-0.07431.10311.04320.08840.0827-1.0602-1.0185-0.11740.84450.04810.00410.7615-0.17520.9207-27.184965.117653.0511
385.3903-6.14584.91519.2175-6.64219.0814-0.2921-1.6558-0.13270.41950.83850.4671-0.4909-0.8076-0.53960.2451-0.06950.05330.46660.00580.509-13.289353.551749.5498
398.8632-0.08824.57356.3144-1.4253.1031-0.2561-0.576-0.05180.29290.16920.4104-0.0991-1.0052-0.04310.4387-0.02650.10870.43740.07420.37050.039238.346751.2863
409.08250.17320.8229.9255-5.08256.3329-0.4462-0.1923-0.4873-0.1120.5866-0.41890.184-1.334-0.06020.3477-0.0567-0.00750.3032-0.0610.2495-14.474148.683140.5924
417.6517-3.56172.19484.2137-1.65372.58610.1789-0.46260.0268-0.15810.05480.0795-0.05850.068-0.20340.26260.00960.01330.2341-0.06560.294-0.500652.392645.9155
426.93792.19853.28313.92640.04585.18440.2807-0.1501-0.43190.0846-0.08890.25620.58430.0121-0.21610.2572-0.02710.06810.2393-0.0640.27611.750742.189937.564
437.398-0.15341.88592.38242.13657.06511.21630.2025-0.73640.1017-0.11150.50960.86860.8109-0.52950.48090.0488-0.04640.19150.17440.43083.671135.111238.9108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 111 )
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 192 )
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 24 )
4X-RAY DIFFRACTION4chain 'B' and (resid 25 through 51 )
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 91 )
6X-RAY DIFFRACTION6chain 'B' and (resid 92 through 111 )
7X-RAY DIFFRACTION7chain 'B' and (resid 112 through 139 )
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 168 )
9X-RAY DIFFRACTION9chain 'B' and (resid 169 through 192 )
10X-RAY DIFFRACTION10chain 'C' and (resid 5 through 70 )
11X-RAY DIFFRACTION11chain 'C' and (resid 71 through 91 )
12X-RAY DIFFRACTION12chain 'C' and (resid 92 through 139 )
13X-RAY DIFFRACTION13chain 'C' and (resid 140 through 192 )
14X-RAY DIFFRACTION14chain 'D' and (resid 4 through 44 )
15X-RAY DIFFRACTION15chain 'D' and (resid 45 through 51 )
16X-RAY DIFFRACTION16chain 'D' and (resid 52 through 71 )
17X-RAY DIFFRACTION17chain 'D' and (resid 72 through 91 )
18X-RAY DIFFRACTION18chain 'D' and (resid 92 through 147 )
19X-RAY DIFFRACTION19chain 'D' and (resid 148 through 192 )
20X-RAY DIFFRACTION20chain 'E' and (resid 5 through 38 )
21X-RAY DIFFRACTION21chain 'E' and (resid 39 through 70 )
22X-RAY DIFFRACTION22chain 'E' and (resid 71 through 78 )
23X-RAY DIFFRACTION23chain 'E' and (resid 79 through 147 )
24X-RAY DIFFRACTION24chain 'E' and (resid 148 through 192 )
25X-RAY DIFFRACTION25chain 'F' and (resid 2 through 24 )
26X-RAY DIFFRACTION26chain 'F' and (resid 25 through 71 )
27X-RAY DIFFRACTION27chain 'F' and (resid 72 through 91 )
28X-RAY DIFFRACTION28chain 'F' and (resid 92 through 192 )
29X-RAY DIFFRACTION29chain 'G' and (resid 5 through 30 )
30X-RAY DIFFRACTION30chain 'G' and (resid 31 through 71 )
31X-RAY DIFFRACTION31chain 'G' and (resid 72 through 91 )
32X-RAY DIFFRACTION32chain 'G' and (resid 92 through 111 )
33X-RAY DIFFRACTION33chain 'G' and (resid 112 through 147 )
34X-RAY DIFFRACTION34chain 'G' and (resid 148 through 192 )
35X-RAY DIFFRACTION35chain 'H' and (resid 4 through 24 )
36X-RAY DIFFRACTION36chain 'H' and (resid 25 through 38 )
37X-RAY DIFFRACTION37chain 'H' and (resid 39 through 51 )
38X-RAY DIFFRACTION38chain 'H' and (resid 52 through 71 )
39X-RAY DIFFRACTION39chain 'H' and (resid 72 through 91 )
40X-RAY DIFFRACTION40chain 'H' and (resid 92 through 111 )
41X-RAY DIFFRACTION41chain 'H' and (resid 112 through 138 )
42X-RAY DIFFRACTION42chain 'H' and (resid 139 through 174 )
43X-RAY DIFFRACTION43chain 'H' and (resid 175 through 192 )

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