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- PDB-5x0n: Regulatory domain of variant C227S AphB from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 5x0n
TitleRegulatory domain of variant C227S AphB from Vibrio vulnificus
ComponentsLysR family transcriptional regulator
KeywordsTRANSCRIPTION / AphB / LysR-type / transcriptional regulator
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
D-Maltodextrin-Binding Protein; domain 2 - #290 / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LysR family transcriptional regulator
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.993 Å
AuthorsSong, S. / Park, N. / Ha, N.-C.
CitationJournal: Mol. Cells / Year: 2017
Title: Crystal Structure of the Regulatory Domain of AphB from Vibrio vulnificus, a Virulence Gene Regulator
Authors: Park, N. / Song, S. / Choi, G. / Jang, K.K. / Jo, I. / Choi, S.H. / Ha, N.-C.
History
DepositionJan 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: LysR family transcriptional regulator
B: LysR family transcriptional regulator
C: LysR family transcriptional regulator
D: LysR family transcriptional regulator
E: LysR family transcriptional regulator
F: LysR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)140,3216
Polymers140,3216
Non-polymers00
Water00
1
A: LysR family transcriptional regulator
D: LysR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)46,7742
Polymers46,7742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-9 kcal/mol
Surface area17730 Å2
MethodPISA
2
B: LysR family transcriptional regulator
C: LysR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)46,7742
Polymers46,7742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-10 kcal/mol
Surface area17560 Å2
MethodPISA
3
E: LysR family transcriptional regulator
F: LysR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)46,7742
Polymers46,7742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-11 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.282, 72.385, 112.211
Angle α, β, γ (deg.)90.00, 118.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
LysR family transcriptional regulator


Mass: 23386.916 Da / Num. of mol.: 6 / Fragment: UNP residues 88-291 / Mutation: C227S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: JS86_04620 / Plasmid: pPROEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: A0A087IWB4

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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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.25M Potassium thiocynate (pH 7), 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.993→38.934 Å / Num. obs: 28983 / % possible obs: 97.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.169 / Net I/av σ(I): 7.19 / Net I/σ(I): 7.19
Reflection shellResolution: 3→3.05 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.14 / Num. unique all: 1459 / % possible all: 90.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DENZOdata reduction
HKL-2000data scaling
HKL-2000data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FHK
Resolution: 2.993→38.934 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 29.75
RfactorNum. reflection% reflection
Rfree0.2911 1478 5.1 %
Rwork0.2366 --
obs0.2394 28983 87.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.993→38.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9167 0 0 0 9167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039396
X-RAY DIFFRACTIONf_angle_d0.60412744
X-RAY DIFFRACTIONf_dihedral_angle_d4.1266441
X-RAY DIFFRACTIONf_chiral_restr0.0451440
X-RAY DIFFRACTIONf_plane_restr0.0041614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9929-3.08950.3849780.33281430X-RAY DIFFRACTION51
3.0895-3.19990.4166870.30411909X-RAY DIFFRACTION67
3.1999-3.32790.35241100.28852112X-RAY DIFFRACTION75
3.3279-3.47930.32921300.26682446X-RAY DIFFRACTION87
3.4793-3.66260.33751430.26442670X-RAY DIFFRACTION94
3.6626-3.89190.31541580.24892759X-RAY DIFFRACTION98
3.8919-4.19210.27561650.22062770X-RAY DIFFRACTION98
4.1921-4.61330.24721450.20782814X-RAY DIFFRACTION99
4.6133-5.27950.2191500.1952851X-RAY DIFFRACTION99
5.2795-6.64620.3061670.23692840X-RAY DIFFRACTION99
6.6462-38.93780.26961450.2192904X-RAY DIFFRACTION98
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)
11.8224-0.3248-0.54032.49380.95081.81970.3627-0.1149-0.4751-0.1397-0.13370.0386-0.29750.02320.4710.33150.0258-0.02980.11480.10.3512-20.6089-25.4613-39.6559
23.2814-0.2348-0.65461.26261.51951.9876-0.2179-0.1217-0.6040.03450.03270.3140.473-0.04840.0070.3264-0.01540.01060.29160.06740.2225-25.7412-18.8665-45.7985
31.7019-0.00360.84161.3313-1.24652.1369-0.138-0.24330.21040.6728-0.25470.193-0.315-0.294-1.22740.35490.09030.14060.2909-0.03710.0973-23.4335-19.4039-34.4804
40.8643-1.0236-0.43622.88870.65421.89270.1517-0.3012-0.01810.97230.2729-0.07780.17190.11110.28420.6418-0.2285-0.1070.45870.05820.3265-32.2963-30.639-30.8724
54.4808-0.04320.27952.7843-1.14972.25350.02150.06890.1991-0.55670.0581-0.59340.55840.58620.13810.42060.05770.08560.2140.05470.2209-14.8319-48.6845-51.6079
61.66430.745-0.35861.2504-0.57940.83910.0227-0.0704-0.0287-0.0881-0.1654-0.33070.38240.28160.15010.35520.05750.03030.23730.05560.2223-15.0625-49.7817-41.4908
70.91510.82480.62450.78820.31971.8225-0.0440.14420.1134-0.4387-0.1752-0.232-0.25030.3181-0.65630.33060.10460.17440.37610.17150.1789-16.7293-42.1169-51.2672
81.3946-0.5143-0.75172.70060.02991.6844-0.1312-0.1509-0.1230.1639-0.30191.0363-0.0331-0.38280.18080.13110.10260.03640.3932-0.05070.2616-29.6956-35.026-37.3475
92.2140.15740.48981.608-0.58620.34790.1295-0.4467-0.07190.46260.36670.0792-0.51710.03090.27240.27030.07250.13040.1666-0.01480.368-33.5334-18.2961-39.7467
100.8893-0.2925-0.16111.59681.09421.81910.12610.1207-0.11160.0395-0.18120.0215-0.17370.079-0.45820.3697-0.00940.02910.50690.00850.1629-44.5364-51.8489-4.7807
112.942-0.73380.30681.4837-0.31431.7444-0.2661-0.21720.54290.43920.1994-0.2938-0.5308-0.0366-0.06490.32720.0082-0.01450.1803-0.00920.1382-44.5665-45.3826-2.6033
120.43850.5991-0.0971.69850.32040.92070.1484-0.2251-0.16750.2058-0.1077-0.2229-0.1091-0.4355-0.12820.19360.1024-0.05550.23920.0660.1639-45.1948-61.62690.1905
131.4857-0.0708-0.14552.3558-0.40421.1490.22310.1746-0.35330.0490.08760.19030.67810.19180.44180.40090.0048-0.14120.1512-0.19720.2176-47.9357-84.5023-13.5254
141.20770.7502-0.90031.3847-0.17091.5769-0.2058-0.02760.0652-0.23390.2058-0.0157-0.0344-0.156-0.06060.29330.09140.03510.20130.03350.1425-47.5554-72.5621-9.2281
150.8254-0.3237-0.11861.4175-0.35380.8994-0.0152-0.19130.06060.41750.14070.1964-0.3394-0.36470.17440.245-0.00480.20540.30010.05960.0611-46.5339-47.92857.1918
161.2394-0.8013-0.18811.15110.28051.426-0.0742-0.07130.05220.23240.12750.1408-0.1061-0.0980.08630.46680.14680.20810.2869-0.06380.0817-37.0188-61.8228-21.4253
172.09241.00760.64351.9472-0.26942.4708-0.16880.4623-0.7586-0.3490.0532-0.33360.87770.1888-0.48930.4350.09140.10680.1016-0.160.2074-39.0693-70.224-24.6569
180.686-1.3937-0.48072.87541.33453.58890.2871-0.23140.32340.7324-0.2924-0.5577-0.0680.5580.38170.4098-0.0992-0.00540.14730.04930.2911-27.1081-58.5381-21.3433
190.5823-0.1165-0.17931.0186-0.20910.8085-0.1391-0.04730.00430.05310.19620.2549-0.1141-0.01210.17380.39680.0122-0.00410.25470.3760.1367-27.9053-55.7881-31.7311
202.33140.2412-0.64312.02560.22421.4114-0.0889-0.20710.39670.33440.21090.5409-0.0635-0.09170.0150.38330.1690.0290.1828-0.0020.2676-52.7676-39.826-21.3927
214.46712.7067-2.43641.64-1.46251.51180.039-0.5419-0.0040.26750.38260.3-0.8329-0.1558-0.22010.42160.06640.16590.35650.04140.3563-52.7126-29.2411-20.9929
220.52380.5013-0.59122.9883-1.66552.27780.07550.23840.12850.7401-0.1593-0.5174-0.6785-0.0618-0.13470.26310.01790.00130.220.02330.2505-41.9822-34.4918-20.4085
232.3912-0.70680.73860.4306-0.21010.44420.44980.2138-0.38890.4092-0.23440.25330.4355-0.1772-0.07130.2925-0.07170.04520.3020.0370.2415-46.9751-46.5222-13.1697
240.4580.1723-0.27360.72780.53961.4809-0.33380.1277-0.71220.1217-0.22450.60780.326-0.771-0.18320.04610.03340.23260.2657-0.10730.3338-51.0524-46.5003-22.5208
252.1769-0.08050.6641.4024-0.34611.2290.11230.68470.2717-0.1238-0.2518-0.00420.17440.1029-0.13170.2540.0676-0.03330.191-0.06690.2517-49.0037-38.5915-27.8229
261.15890.1724-0.02760.7946-0.55511.0152-0.2256-0.0169-0.1429-0.2145-0.0424-0.18120.456-0.1021-0.71350.22680.11020.3740.2750.05350.157-32.7631-64.6886-32.7453
271.5723-1.136-0.60753.2457-2.34423.45250.0716-0.0980.02830.4889-0.1305-0.5718-0.47010.46050.49430.01390.0436-0.2290.37920.18370.7263-0.6154-36.6362-38.4483
280.8853-0.477-0.11770.607-0.06331.5782-0.0386-0.15530.13510.4465-0.1068-0.5393-0.26050.81740.21370.3726-0.1228-0.12360.501-0.01410.70825.7723-29.0855-32.3209
292.162-0.03520.07041.5818-1.56861.8975-0.11240.40570.0086-0.03530.0684-0.2616-0.22790.18760.16810.2756-0.0509-0.02720.32490.00570.2304-7.6133-12.7717-47.7359
300.4449-0.0255-0.04522.47370.56121.0097-0.12320.31570.00960.4661-0.0168-0.80990.05660.28510.63170.26350.0240.04230.4310.2490.53016.5179-29.0251-42.3947
311.75180.1443-0.48081.8603-0.57321.99350.0208-0.13090.03810.1195-0.1207-0.2293-0.0260.28310.0210.31960.0425-0.130.26120.04140.2842-35.9116-91.142217.4393
320.4822-0.08490.26951.948-0.30071.06170.0458-0.10910.11940.0784-0.1127-0.0377-0.387-0.1343-0.07780.23450.02790.01350.21310.06850.3193-40.9386-69.362321.0155
331.4711-0.8162-0.03611.8947-0.00212.6447-0.0062-0.2262-0.2690.21520.1484-0.00320.04890.0977-0.01640.3244-0.0376-0.07680.23720.04240.2483-39.5459-66.693626.792
341.09690.29920.3473.7029-0.49830.7971-0.2167-0.1632-0.236-0.20750.13870.35090.269-0.3955-0.02040.2987-0.06980.0090.2585-0.00460.2041-43.6682-91.545610.0563
351.51350.1027-0.31882.22951.49163.1731-0.1232-0.09410.41270.2942-0.4724-0.2440.3707-0.1544-0.41730.470.0445-0.15890.4707-0.00680.4042-24.7164-77.5233.1756
362.1880.89260.01231.9744-0.87123.4784-0.1339-0.35470.05030.0185-0.0549-0.3138-0.18260.12940.07680.40140.0172-0.33470.34280.04690.49-25.0271-68.722636.2328
370.33960.5412-0.62291.35-0.34051.9682-0.17050.08730.14940.2541-0.597-0.72090.16530.3013-0.4050.50050.0119-0.30820.41640.01510.5699-13.439-79.587534.6515
381.1124-1.513-0.13552.4266-0.52341.3892-0.106-0.3363-0.7226-0.0550.12820.11640.09710.1217-0.61090.4371-0.047-0.21470.36030.28120.3762-34.9647-101.877538.5416
390.4841-0.22590.73410.784-0.84051.5296-0.3029-0.10830.0494-0.24750.0285-0.33310.46740.48760.00060.40630.1153-0.10840.49410.09940.2869-27.3426-104.794332.1216
403.9958-0.74610.40830.5711-0.40491.619-0.21420.22151.16860.0340.1212-0.1571-0.6422-0.12510.23910.32960.0817-0.07110.36610.01390.2266-35.0294-93.267433.4749
412.53830.51490.22662.1011-1.47712.81420.0132-0.85990.40490.5411-0.2206-0.1411-0.0351-0.1466-0.00180.39880.1693-0.14530.4192-0.22420.4656-32.8125-100.383842.3297
420.16-0.1851-0.44081.98210.07621.3893-0.0157-0.5011-0.01010.3850.1106-1.1548-0.54160.190.18950.54950.0512-0.23850.3206-0.07670.5915-15.3086-74.251440.4597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 92 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 116 )
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 144 )
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 160 )
5X-RAY DIFFRACTION5chain 'A' and (resid 161 through 173 )
6X-RAY DIFFRACTION6chain 'A' and (resid 174 through 227 )
7X-RAY DIFFRACTION7chain 'A' and (resid 228 through 253 )
8X-RAY DIFFRACTION8chain 'A' and (resid 254 through 276 )
9X-RAY DIFFRACTION9chain 'A' and (resid 277 through 288 )
10X-RAY DIFFRACTION10chain 'B' and (resid 91 through 106 )
11X-RAY DIFFRACTION11chain 'B' and (resid 107 through 137 )
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 171 )
13X-RAY DIFFRACTION13chain 'B' and (resid 172 through 188 )
14X-RAY DIFFRACTION14chain 'B' and (resid 189 through 261 )
15X-RAY DIFFRACTION15chain 'B' and (resid 262 through 288 )
16X-RAY DIFFRACTION16chain 'C' and (resid 90 through 105 )
17X-RAY DIFFRACTION17chain 'C' and (resid 106 through 126 )
18X-RAY DIFFRACTION18chain 'C' and (resid 127 through 144 )
19X-RAY DIFFRACTION19chain 'C' and (resid 145 through 160 )
20X-RAY DIFFRACTION20chain 'C' and (resid 161 through 171 )
21X-RAY DIFFRACTION21chain 'C' and (resid 172 through 181 )
22X-RAY DIFFRACTION22chain 'C' and (resid 182 through 214 )
23X-RAY DIFFRACTION23chain 'C' and (resid 215 through 229 )
24X-RAY DIFFRACTION24chain 'C' and (resid 230 through 247 )
25X-RAY DIFFRACTION25chain 'C' and (resid 248 through 261 )
26X-RAY DIFFRACTION26chain 'C' and (resid 262 through 290 )
27X-RAY DIFFRACTION27chain 'D' and (resid 90 through 137 )
28X-RAY DIFFRACTION28chain 'D' and (resid 138 through 152 )
29X-RAY DIFFRACTION29chain 'D' and (resid 153 through 247 )
30X-RAY DIFFRACTION30chain 'D' and (resid 248 through 288 )
31X-RAY DIFFRACTION31chain 'E' and (resid 90 through 140 )
32X-RAY DIFFRACTION32chain 'E' and (resid 141 through 185 )
33X-RAY DIFFRACTION33chain 'E' and (resid 186 through 261 )
34X-RAY DIFFRACTION34chain 'E' and (resid 262 through 290 )
35X-RAY DIFFRACTION35chain 'F' and (resid 91 through 106 )
36X-RAY DIFFRACTION36chain 'F' and (resid 107 through 127 )
37X-RAY DIFFRACTION37chain 'F' and (resid 128 through 156 )
38X-RAY DIFFRACTION38chain 'F' and (resid 157 through 179 )
39X-RAY DIFFRACTION39chain 'F' and (resid 180 through 214 )
40X-RAY DIFFRACTION40chain 'F' and (resid 215 through 245 )
41X-RAY DIFFRACTION41chain 'F' and (resid 246 through 260 )
42X-RAY DIFFRACTION42chain 'F' and (resid 261 through 288 )

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  • 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

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