[English] 日本語
Yorodumi
- PDB-5x0n: Regulatory domain of variant C227S AphB from Vibrio vulnificus -

+
Open data


ID or keywords:

Loading...

-
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 )

+
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://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