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- PDB-5vlm: Crystal structure of EilR in complex with crystal violet -

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Basic information

Entry
Database: PDB / ID: 5vlm
TitleCrystal structure of EilR in complex with crystal violet
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
CRYSTAL VIOLET / EilR repressor
Similarity search - Component
Biological speciesEnterobacter lignolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.403 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)176,65816
Polymers173,6788
Non-polymers2,9808
Water00
1
A: Regulatory protein TetR
B: Regulatory protein TetR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1654
Polymers43,4202
Non-polymers7452
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-15 kcal/mol
Surface area17660 Å2
MethodPISA
2
C: Regulatory protein TetR
D: Regulatory protein TetR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1654
Polymers43,4202
Non-polymers7452
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-15 kcal/mol
Surface area17480 Å2
MethodPISA
3
E: Regulatory protein TetR
F: Regulatory protein TetR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1654
Polymers43,4202
Non-polymers7452
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-18 kcal/mol
Surface area17820 Å2
MethodPISA
4
G: Regulatory protein TetR
H: Regulatory protein TetR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1654
Polymers43,4202
Non-polymers7452
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-16 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.397, 79.229, 105.579
Angle α, β, γ (deg.)90.00, 97.10, 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) / Gene: Entcl_2353 / Production host: Escherichia coli (E. coli) / References: UniProt: E3G817
#2: Chemical
ChemComp-CVI / CRYSTAL VIOLET


Mass: 372.526 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C25H30N3 / Comment: antifungal, antibiotic*YM

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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: 2.33 Å3/Da / Density % sol: 47.15 %
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: 3.4→50 Å / Num. obs: 20683 / % possible obs: 93.4 % / Redundancy: 2.9 % / Net I/σ(I): 3.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2650: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.403→48.644 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.61
RfactorNum. reflection% reflection
Rfree0.2717 2019 10.06 %
Rwork0.2049 --
obs0.2115 20065 90.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.403→48.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12000 0 224 0 12224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212459
X-RAY DIFFRACTIONf_angle_d0.49116838
X-RAY DIFFRACTIONf_dihedral_angle_d8.6447316
X-RAY DIFFRACTIONf_chiral_restr0.0331826
X-RAY DIFFRACTIONf_plane_restr0.0022171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4028-3.48790.35481200.281110X-RAY DIFFRACTION79
3.4879-3.58220.36941310.28211149X-RAY DIFFRACTION81
3.5822-3.68760.29911310.25971171X-RAY DIFFRACTION84
3.6876-3.80660.34641400.24721197X-RAY DIFFRACTION84
3.8066-3.94250.32641400.24831197X-RAY DIFFRACTION85
3.9425-4.10030.32051350.22971235X-RAY DIFFRACTION87
4.1003-4.28680.25751460.19761265X-RAY DIFFRACTION91
4.2868-4.51270.26921420.19321356X-RAY DIFFRACTION95
4.5127-4.79520.2131610.17841373X-RAY DIFFRACTION97
4.7952-5.1650.23271450.19441383X-RAY DIFFRACTION97
5.165-5.68410.29911580.20421400X-RAY DIFFRACTION97
5.6841-6.5050.31391540.21771393X-RAY DIFFRACTION97
6.505-8.18920.24851580.17861401X-RAY DIFFRACTION97
8.1892-48.64860.19321580.14471416X-RAY DIFFRACTION95
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)
16.60230.3343-0.56096.918-6.91698.1827-0.7448-1.0776-0.20040.6610.2132-1.14090.02650.06650.34180.6140.0390.021.0089-0.07980.3451-25.30538.65527.0378
24.5366-3.69924.79715.0337-3.71055.09640.05890.1153-0.13780.2455-0.2157-0.25970.0621.37050.25830.37670.1851-0.0420.79830.12050.2605-17.167812.72072.6915
31.63510.41681.76864.881-0.246.571-0.6495-0.4695-0.27040.31680.4007-0.73980.56890.75670.03660.3865-0.0239-0.10250.4490.24890.5303-27.49536.89480.1758
41.17550.4809-0.10460.844-0.43690.24830.1697-0.43570.40690.2026-0.48380.5806-0.0118-0.5280.30351.19310.45630.56041.3519-0.30141.0548-51.238717.51743.3506
53.99640.31361.42092.4655-1.56623.09520.2387-0.24730.0094-0.0013-0.1340.2890.0981-0.1652-0.12910.344-0.04910.04450.4748-0.09370.2323-42.792414.7475-8.3394
66.91243.52640.10235.3672-1.66313.82960.0890.01760.7188-0.0971-0.36720.0690.20610.27670.23570.2918-0.0730.07910.50340.00280.2379-42.511421.916-16.5391
77.5936-0.103-3.54885.5033-3.58085.3892-0.1137-0.60531.02490.664-0.1210.48680.0879-0.0391-0.1410.37130.0140.12350.6614-0.10010.4618-51.873625.5544-13.729
83.7366-0.9072.48845.4961-2.18784.5496-0.50960.46630.4863-0.1111-0.4026-0.1233-0.37470.85370.60960.43870.0863-0.12110.9291-0.08650.531-19.953625.1067-43.9089
92.70010.99-2.79950.8512-1.39013.1882-0.10170.64620.00990.2305-0.3725-0.425-0.88011.27360.19310.5071-0.16490.0710.84450.27060.5893-13.302523.4463-38.1878
103.39021.3667-0.39357.784-1.79486.82350.52520.20540.50330.2601-0.1135-0.3218-0.3373-0.593-0.11410.3160.04090.15140.35670.21370.3964-28.768925.2171-36.5626
110.65580.0918-0.32010.4068-0.09410.1632-0.12260.32180.2311-0.6634-0.11090.5811-0.5497-0.67830.41690.8309-0.1062-0.42231.22640.25580.653-47.741223.1817-43.1088
126.5222-1.60620.37773.28560.18163.46150.45370.36940.4942-0.1826-0.4106-0.0442-0.1715-0.2931-0.07370.27960.02520.01290.5220.10120.1976-40.201223.781-30.9608
134.2131-1.1864-0.92884.44140.08353.11380.1134-0.1171-0.2663-0.2851-0.27840.19080.0579-0.97360.19830.2729-0.09040.0640.4764-0.04620.1991-46.844616.5599-24.3643
147.5436-2.99452.09032.76-3.1678.342-0.09780.3468-0.19360.5115-0.187-0.27530.21270.50610.1310.5175-0.1182-0.02540.5775-0.05650.4427.022328.226810.1055
155.59510.49961.6781.4279-1.28072.87020.2342-0.11770.63050.3554-0.10540.5109-0.1903-0.0388-0.08240.33840.08860.05050.7326-0.09550.5034-7.269237.1869-3.1254
164.63730.52371.07221.8772-0.53733.34180.07030.2671.1746-0.00920.26030.3972-0.3614-0.5202-0.34590.39040.09950.07840.35560.07860.5703-6.695843.8778-12.9436
177.90326.9727-5.86727.1282-5.14987.8331-0.57021.1453-1.086-0.9263-0.0298-0.7520.31431.18250.33310.62840.1601-0.22321.2654-0.13270.698121.953430.5755-38.3628
186.84951.0535-5.85854.2957-2.71029.11470.3974-0.2514-0.7016-0.2664-0.9038-0.28490.15520.6710.45830.37890.1317-0.16930.5408-0.1370.524926.039227.8898-31.1106
195.175-0.4145-1.17546.62261.07273.26940.61510.9778-0.4216-0.0274-0.18610.3341-0.1150.4139-0.17460.4510.0438-0.09880.3519-0.16610.285212.030735.2132-31.4328
206.2881-4.2851-0.57949.61-3.79456.39980.09620.6425-0.1454-0.3394-0.00370.4449-0.2205-0.892-0.13750.39630.1583-0.16080.5556-0.11160.4934-8.84139.1277-37.0249
211.8997-2.8874-1.46914.62082.91563.15760.34920.4497-0.8096-0.0997-0.67520.65470.2518-0.6187-0.23070.36290.052-0.25470.5738-0.24080.597-2.797128.678-31.0701
226.3128-0.3491-0.86534.4862-0.34884.65770.0864-0.0215-0.01070.0238-0.06610.2395-0.2439-0.6331-0.0280.2493-0.0622-0.00910.3283-0.04720.2576-2.794538.2549-23.429
235.19421.2533-0.58523.33260.05622.1506-0.2209-0.1229-0.06720.16820.2578-0.75670.0934-0.253-0.02860.34170.05190.02040.21750.00280.3443-42.920268.7226-12.3649
241.65240.19830.54633.6974-0.59311.9599-0.1369-0.40060.1091-0.73780.18790.12040.3292-0.0015-0.00580.3584-0.14990.04150.5181-0.07130.207-57.971960.5887-24.4817
254.2798-1.19650.19391.88071.41091.39850.11790.41540.967-2.0006-0.5185-1.41650.74560.14260.43231.11820.08230.42641.4592-0.01040.6835-36.183673.5263-59.7118
267.61732.1445-4.3487.945-4.49424.0054-0.23951.28130.52050.42370.3558-1.3541-1.9948-1.0922-0.16521.0105-0.00890.09210.9317-0.03310.756-30.241576.6002-53.1174
270.1968-0.10970.10110.29980.34651.48160.02440.03230.0030.0479-0.04480.0440.0531-0.0132-0.42661.0059-0.34360.17370.5684-0.24090.2775-44.145670.997-50.7177
288.33571.12661.34470.1520.1872.2647-0.01650.1848-0.0998-0.9658-0.04022.27980.8388-0.776-0.1871.2612-0.5598-0.13290.984-0.39651.355-59.228156.6264-55.2395
292.68580.55430.80350.40720.02492.0427-0.2113-0.0593-0.2605-0.37280.2368-0.03220.25560.0377-0.07440.8832-0.29680.04830.7012-0.13070.2846-54.238564.2848-44.1351
305.17361.01421.81690.9354-0.50721.90750.31110.2536-0.9565-0.7143-0.1315-0.18920.7911-0.5143-0.19670.7592-0.20460.0930.4557-0.12970.2624-56.465656.7249-35.2249
315.73213.42923.4093.06990.10868.078-0.6056-1.21821.04050.48020.32111.7475-0.4075-1.20420.15010.7070.24860.13890.96980.26790.9301-13.850753.914-43.3487
327.22331.4577-6.76537.7476-0.32677.7505-0.76281.1432-0.0404-0.05830.57031.7885-0.3802-0.87940.10350.6256-0.0587-0.2630.57590.25970.9126-19.649247.7868-52.3638
331.8628-1.8759-0.50443.43930.54471.48160.5304-0.21561.12390.58340.69520.5329-0.4836-0.1055-0.75721.55780.6637-0.09520.8342-0.11461.6881-21.392959.5647-48.3391
344.41813.33813.26947.96491.9289.09970.1994-1.29720.97780.6420.15510.56140.0026-1.3991-0.31280.3121-0.15270.01760.7361-0.00680.6368-5.292151.956-50.0549
356.6062-2.8862-0.066.02141.46654.7601-0.7905-0.37040.24040.10041.03420.06-0.06370.13830.14420.95670.0285-0.18970.3041-0.00060.32113.681141.7429-44.4717
362.7159-0.24410.55042.82060.75243.40630.0831-0.33610.251-0.25090.60940.3511-0.40470.1395-0.36270.4689-0.1559-0.09820.55870.16450.6285.596147.3024-55.2161
376.7542.04751.14122.05730.12023.49460.08590.1056-0.7164-0.21470.0113-0.14990.0972-0.1639-0.16540.6526-0.3087-0.03120.6856-0.03470.18988.091539.4942-62.4416
385.58170.43314.33178.85542.97476.3780.73770.0243-0.91420.22530.1550.39990.1668-0.0805-0.59840.5367-0.2118-0.09820.4861-0.00850.360916.460735.1268-57.5326
397.7191-0.85382.55147.56186.34558.01010.17530.3467-0.6021-0.27-0.8691.93541.4085-0.28070.40521.03420.06790.12990.658-0.08070.6797-8.175136.2263-95.9397
404.8538-0.7911-0.50964.6355-1.08473.7333-0.31560.1925-0.0187-0.68620.1880.29610.2665-0.08250.17690.5417-0.17130.0340.5258-0.02090.2357-9.205437.7725-88.5575
411.96182.34452.18535.29332.41543.4717-0.0350.5095-0.869-0.91450.521-1.42630.02420.4252-0.11840.8993-0.38410.26970.5106-0.25070.749519.905338.6446-87.2605
422.8205-2.71640.54633.66061.10655.24970.1647-0.3018-0.3625-0.03280.3866-0.3148-0.14130.1222-0.5750.4071-0.083-0.07740.22220.00610.39279.544538.5153-75.2469
437.1134-2.05553.0684.0298-1.09163.618-0.3187-0.54331.495-0.47210.6472-1.0315-0.55940.3899-0.20850.4825-0.21760.04380.5003-0.29220.612917.965247.7142-68.8061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 70 )
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 78 )
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 147 )
6X-RAY DIFFRACTION6chain 'A' and (resid 148 through 174 )
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 192 )
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 24 )
9X-RAY DIFFRACTION9chain 'B' and (resid 25 through 53 )
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 70 )
11X-RAY DIFFRACTION11chain 'B' and (resid 71 through 78 )
12X-RAY DIFFRACTION12chain 'B' and (resid 79 through 147 )
13X-RAY DIFFRACTION13chain 'B' and (resid 148 through 192 )
14X-RAY DIFFRACTION14chain 'C' and (resid 6 through 72 )
15X-RAY DIFFRACTION15chain 'C' and (resid 73 through 147 )
16X-RAY DIFFRACTION16chain 'C' and (resid 148 through 192 )
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 24 )
18X-RAY DIFFRACTION18chain 'D' and (resid 25 through 51 )
19X-RAY DIFFRACTION19chain 'D' and (resid 52 through 71 )
20X-RAY DIFFRACTION20chain 'D' and (resid 72 through 85 )
21X-RAY DIFFRACTION21chain 'D' and (resid 86 through 94 )
22X-RAY DIFFRACTION22chain 'D' and (resid 95 through 192 )
23X-RAY DIFFRACTION23chain 'E' and (resid 5 through 111 )
24X-RAY DIFFRACTION24chain 'E' and (resid 112 through 192 )
25X-RAY DIFFRACTION25chain 'F' and (resid 2 through 24 )
26X-RAY DIFFRACTION26chain 'F' and (resid 25 through 51 )
27X-RAY DIFFRACTION27chain 'F' and (resid 52 through 70 )
28X-RAY DIFFRACTION28chain 'F' and (resid 71 through 78 )
29X-RAY DIFFRACTION29chain 'F' and (resid 79 through 147 )
30X-RAY DIFFRACTION30chain 'F' and (resid 148 through 192 )
31X-RAY DIFFRACTION31chain 'G' and (resid 5 through 23 )
32X-RAY DIFFRACTION32chain 'G' and (resid 24 through 38 )
33X-RAY DIFFRACTION33chain 'G' and (resid 39 through 51 )
34X-RAY DIFFRACTION34chain 'G' and (resid 52 through 70 )
35X-RAY DIFFRACTION35chain 'G' and (resid 71 through 85 )
36X-RAY DIFFRACTION36chain 'G' and (resid 86 through 147 )
37X-RAY DIFFRACTION37chain 'G' and (resid 148 through 174 )
38X-RAY DIFFRACTION38chain 'G' and (resid 175 through 192 )
39X-RAY DIFFRACTION39chain 'H' and (resid 2 through 24 )
40X-RAY DIFFRACTION40chain 'H' and (resid 25 through 70 )
41X-RAY DIFFRACTION41chain 'H' and (resid 71 through 78 )
42X-RAY DIFFRACTION42chain 'H' and (resid 79 through 168 )
43X-RAY DIFFRACTION43chain 'H' and (resid 169 through 192 )

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