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- PDB-8hdj: Periplasmic domain of RsgI2 of Clostridium thermocellum -

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Basic information

Entry
Database: PDB / ID: 8hdj
TitlePeriplasmic domain of RsgI2 of Clostridium thermocellum
Components
  • Anti-sigma-I factor RsgI2
  • Periplasmic domain of RsgI2
KeywordsSIGNALING PROTEIN / anti-sigmaI
Function / homology
Function and homology information


cellulose binding / carbohydrate metabolic process / metal ion binding / plasma membrane
Similarity search - Function
Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / CBM2/CBM3, carbohydrate-binding domain superfamily
Similarity search - Domain/homology
Anti-sigma-I factor RsgI2
Similarity search - Component
Biological speciesAcetivibrio thermocellus DSM 1313 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChen, C. / Dong, S. / Feng, Y.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2023
Title: Essential autoproteolysis of bacterial anti-sigma factor RsgI for transmembrane signal transduction.
Authors: Chen, C. / Dong, S. / Yu, Z. / Qiao, Y. / Li, J. / Ding, X. / Li, R. / Lin, J. / Bayer, E.A. / Liu, Y.J. / Cui, Q. / Feng, Y.
History
DepositionNov 4, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic domain of RsgI2
B: Anti-sigma-I factor RsgI2
C: Periplasmic domain of RsgI2
D: Anti-sigma-I factor RsgI2
E: Periplasmic domain of RsgI2
F: Anti-sigma-I factor RsgI2
G: Periplasmic domain of RsgI2
H: Anti-sigma-I factor RsgI2


Theoretical massNumber of molelcules
Total (without water)76,5708
Polymers76,5708
Non-polymers00
Water8,665481
1
A: Periplasmic domain of RsgI2
B: Anti-sigma-I factor RsgI2


Theoretical massNumber of molelcules
Total (without water)19,1432
Polymers19,1432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-11 kcal/mol
Surface area8340 Å2
MethodPISA
2
C: Periplasmic domain of RsgI2
D: Anti-sigma-I factor RsgI2


Theoretical massNumber of molelcules
Total (without water)19,1432
Polymers19,1432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-11 kcal/mol
Surface area8370 Å2
MethodPISA
3
E: Periplasmic domain of RsgI2
F: Anti-sigma-I factor RsgI2


Theoretical massNumber of molelcules
Total (without water)19,1432
Polymers19,1432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-11 kcal/mol
Surface area8650 Å2
MethodPISA
4
G: Periplasmic domain of RsgI2
H: Anti-sigma-I factor RsgI2


Theoretical massNumber of molelcules
Total (without water)19,1432
Polymers19,1432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-11 kcal/mol
Surface area8910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.090, 101.530, 86.360
Angle α, β, γ (deg.)90.000, 92.930, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-110-

HOH

21C-104-

HOH

31D-333-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31(chain E and resid 88 through 97)
41(chain G and resid 88 through 97)
12(chain B and (resid 98 through 131 or resid 133...
22(chain D and (resid 98 through 129 or (resid 130...
32(chain F and (resid 98 through 129 or (resid 130...
42(chain H and (resid 98 through 129 or (resid 130...

NCS ensembles :
ID
1
2

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Components

#1: Protein/peptide
Periplasmic domain of RsgI2


Mass: 1516.564 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein
Anti-sigma-I factor RsgI2


Mass: 17625.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Sequence reference for DSM 1313 is not available in Uniprot at the time of biocuration. Current sequence reference is from uniprot id A3DC27.
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3DC27
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate monohydrate, pH 6.0, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.1
ReflectionResolution: 1.85→24.84 Å / Num. obs: 54750 / % possible obs: 99.4 % / Redundancy: 3.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.049 / Rrim(I) all: 0.089 / Net I/σ(I): 9.3 / Num. measured all: 169195 / Scaling rejects: 85
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.892.70.266907833710.8360.1970.3333.499.6
9.06-24.842.90.09910743730.9630.0670.1213.976.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AFDB:A3DC27F1

Resolution: 1.85→24.35 Å / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 25.6 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2378 2078 3.8 %
Rwork0.2188 52701 -
obs0.2222 54748 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.7 Å2 / Biso mean: 27.5182 Å2 / Biso min: 7.83 Å2
Refinement stepCycle: final / Resolution: 1.85→24.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 0 481 5461
Biso mean---38.94 -
Num. residues----652
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A180X-RAY DIFFRACTION10.964TORSIONAL
12C180X-RAY DIFFRACTION10.964TORSIONAL
13E180X-RAY DIFFRACTION10.964TORSIONAL
14G180X-RAY DIFFRACTION10.964TORSIONAL
21B2789X-RAY DIFFRACTION10.964TORSIONAL
22D2789X-RAY DIFFRACTION10.964TORSIONAL
23F2789X-RAY DIFFRACTION10.964TORSIONAL
24H2789X-RAY DIFFRACTION10.964TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8505-1.89680.3221570.303372796
1.8968-1.94810.30711310.2897375496
1.9481-2.00540.27981430.2667376696
2.0054-2.07010.25661430.2569377096
2.0701-2.1440.2631370.2564376996
2.144-2.22980.25731540.2526376896
2.2298-2.33120.30031360.2464379896
2.3312-2.4540.25361480.2461374496
2.454-2.60760.21931420.2423378996
2.6076-2.80860.22311450.2251372695
2.8086-3.09080.23681370.2216379296
3.0908-3.53690.22921400.2059375596
3.5369-4.45160.19631520.1734379296
4.4516-24.350.2261400.1902375194
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)
12.58170.28630.38442.41490.08373.2834-0.1512-0.1641-0.03710.10880.21270.05730.04110.11160.03220.10020.01190.01060.15060.00080.131833.395420.885318.3681
22.086-0.0021-0.04032.33990.73283.27030.0805-0.11160.3313-0.0012-0.01840.0027-0.1213-0.17160.08120.08470.0023-0.00260.1671-0.00330.115328.194423.504619.1046
31.3236-0.6115-0.83571.78970.7062.327-0.04670.4208-0.068-0.283-0.13940.23370.0631-0.65520.05930.1652-0.0251-0.00290.34030.02220.134923.809617.565611.2875
42.5838-1.84342.0836.8961-3.59253.21850.13060.9549-0.1884-0.6509-0.5498-0.6265-0.30680.540.03050.4909-0.2260.31220.4216-0.1320.209532.46738.08233.9269
52.85270.1835-0.59152.82580.58331.3587-0.0047-0.26680.04740.24410.0065-0.13330.4346-0.1153-0.01520.1686-0.0312-0.02630.1576-0.00020.106333.438412.469922.2239
62.6992-0.1758-0.80491.05560.25561.64870.0031-0.09640.2080.15240.1445-0.1748-0.02280.1563-0.07170.1255-0.05610.01590.1328-0.02410.138943.624420.68916.0862
71.5957-0.253-0.31151.1974-0.13791.3969-0.13060.1205-0.1593-0.03240.1538-0.243-0.038-0.0528-0.04260.1589-0.0064-0.0170.2095-0.03440.145648.555613.48159.5051
81.7342-0.06770.65442.8364-0.9444.87690.1123-0.0758-0.0827-0.10750.06340.2898-0.06060.49430.13980.05490.00690.03550.2154-0.02820.181237.0018-26.247917.9921
92.5027-0.52321.19011.9067-0.59854.48450.14190.0246-0.24850.03520.05450.02810.15290.1024-0.13290.10120.0080.00670.22670.00320.13542.2916-28.705618.9287
102.5359-0.9099-0.372.0065-0.20572.51930.03560.55970.0184-0.2893-0.1477-0.2116-0.1630.75530.04120.1711-0.04610.02420.3829-0.0060.154345.004-20.752210.1705
113.19780.55961.13380.9758-0.78822.2308-0.007-0.0727-0.17860.09630.09390.0451-0.0725-0.046-0.02720.1272-0.02540.0440.1318-0.01780.12130.8732-22.792318.3838
122.5669-1.0417-1.00391.70360.37372.1782-0.0460.19670.10980.06220.05690.21450.04680.0311-0.07030.1510.01110.02560.19030.00720.139121.9299-18.93210.1119
132.67150.08121.16192.1557-0.63114.5093-0.1356-0.04630.40870.0795-0.13120.13970.3323-0.43150.16180.15820.00050.02840.092-0.00880.15468.5137-1.564224.9205
141.88990.08411.02892.19620.00612.69740.0187-0.12350.0655-0.30540.17090.1443-0.0549-0.226-0.09760.11710.011-0.00520.1614-0.00520.10957.27883.47424.5512
151.2217-1.1653-0.21232.38-0.40913.2944-0.0834-0.19020.24480.1742-0.0952-0.1569-0.6227-0.05890.13510.1771-0.0221-0.00850.1685-0.01620.141713.88397.363931.8459
161.15280.4776-1.00472.60410.99661.6873-0.1108-0.1138-0.2776-0.04470.2265-0.1967-0.43830.3597-0.08290.14570.00190.04520.1653-0.00240.13616.3885-4.575829.8854
172.36240.66671.55352.05721.22323.47510.07810.4617-0.1444-0.5110.0354-0.5899-0.16440.44570.06760.2091-0.02590.08430.17280.01850.176319.9117-1.69919.2335
181.20750.7703-0.62821.5201-0.56872.98810.0909-0.1452-0.0129-0.2218-0.06660.04750.0762-0.40410.00470.14190.00180.03310.1983-0.00340.1347.6743-9.615426.2128
192.0143-0.03381.11014.3696-0.27361.52430.00350.057-0.18850.01730.27880.07170.4165-0.1553-0.16520.1438-0.05050.01880.1505-0.01560.10039.2743-17.819929.8353
201.42360.490.59782.16851.55431.14730.2292-0.4204-0.24340.5837-0.22910.04010.3043-0.5589-0.01280.2107-0.03390.03380.19830.0350.14958.1588-15.987839.1133
211.2395-0.01540.22211.8078-0.58211.6169-0.0169-0.4758-0.20810.24320.1473-0.23460.03380.0098-0.06950.17150.00980.02080.1434-0.00830.137417.1549-14.516437.1244
224.55-2.22360.04521.95120.30933.45530.2468-0.4244-0.37150.46060.3572-0.1761-0.3163-0.08391.48950.13370.12810.23840.199-0.17850.176823.2615-16.508324.4969
231.9127-0.23110.0382.06150.67592.89810.01540.06740.2458-0.17910.032-0.3018-0.31520.230.10070.18230.01120.01450.0782-0.02250.136962.2248-4.186324.5473
242.1216-0.3322-0.56672.03790.18073.1794-0.0058-0.0314-0.0539-0.24050.0753-0.24730.27820.24260.01930.15650.02380.02860.15590.00140.125463.2904-8.799224.6476
251.174-0.74850.37381.90970.32463.1492-0.2155-0.0448-0.18770.1936-0.04630.09230.57060.17950.21360.2322-0.02180.05630.12780.01770.145456.7197-12.749132.0172
262.4542-1.20322.7170.9666-1.5473.1070.0511-0.9220.79070.3348-0.14710.0557-0.1511-0.99060.0850.16610.10350.05080.5266-0.15440.248348.1876-2.509739.4323
274.17470.63430.57272.4964-0.22272.7771-0.0108-0.2596-0.0988-0.7471-0.2979-0.03150.06120.1133-0.40140.30280.03990.02820.04360.03910.09458.56790.646922.0907
283.1824-0.2465-1.52893.8259-1.66525.052-0.04080.26320.0529-0.76-0.36380.3720.3851-0.7532-0.0840.2325-0.059-0.0280.1769-0.03630.141950.7487-3.6819.0486
292.07630.32390.51292.19861.18212.47850.0641-0.18580.3052-0.32530.0161-0.1101-0.26980.36980.02030.1254-0.00230.02640.19720.03440.143262.84494.277726.2328
302.1086-0.0767-0.67784.54680.80841.65530.05550.13150.279-0.1170.1476-0.158-0.3006-0.0401-0.17950.1645-0.03060.01710.16440.01540.136461.274212.438229.9104
311.8621-0.936-0.22492.4011-1.12471.5088-0.1546-0.31980.25020.45990.1554-0.1574-0.33320.1288-0.02340.2374-0.0095-0.02210.1226-0.02140.144759.417710.190138.5265
321.8960.0738-0.10340.0177-0.15610.84920.51730.14410.41320.4904-0.2153-0.17910.4236-0.2366-0.1670.2762-0.0392-0.04430.1683-0.00930.369546.251710.127523.0972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 88 through 97 )A88 - 97
2X-RAY DIFFRACTION2chain 'B' and (resid 98 through 117 )B98 - 117
3X-RAY DIFFRACTION3chain 'B' and (resid 118 through 148 )B118 - 148
4X-RAY DIFFRACTION4chain 'B' and (resid 149 through 156 )B149 - 156
5X-RAY DIFFRACTION5chain 'B' and (resid 157 through 192 )B157 - 192
6X-RAY DIFFRACTION6chain 'B' and (resid 193 through 227 )B193 - 227
7X-RAY DIFFRACTION7chain 'B' and (resid 228 through 258 )B228 - 258
8X-RAY DIFFRACTION8chain 'C' and (resid 88 through 97 )C88 - 97
9X-RAY DIFFRACTION9chain 'D' and (resid 98 through 117 )D98 - 117
10X-RAY DIFFRACTION10chain 'D' and (resid 118 through 156 )D118 - 156
11X-RAY DIFFRACTION11chain 'D' and (resid 157 through 227 )D157 - 227
12X-RAY DIFFRACTION12chain 'D' and (resid 228 through 259 )D228 - 259
13X-RAY DIFFRACTION13chain 'E' and (resid 87 through 97 )E87 - 97
14X-RAY DIFFRACTION14chain 'F' and (resid 98 through 117 )F98 - 117
15X-RAY DIFFRACTION15chain 'F' and (resid 118 through 148 )F118 - 148
16X-RAY DIFFRACTION16chain 'F' and (resid 149 through 175 )F149 - 175
17X-RAY DIFFRACTION17chain 'F' and (resid 176 through 192 )F176 - 192
18X-RAY DIFFRACTION18chain 'F' and (resid 193 through 215 )F193 - 215
19X-RAY DIFFRACTION19chain 'F' and (resid 216 through 228 )F216 - 228
20X-RAY DIFFRACTION20chain 'F' and (resid 229 through 241 )F229 - 241
21X-RAY DIFFRACTION21chain 'F' and (resid 242 through 248 )F242 - 248
22X-RAY DIFFRACTION22chain 'F' and (resid 249 through 258 )F249 - 258
23X-RAY DIFFRACTION23chain 'G' and (resid 87 through 97 )G87 - 97
24X-RAY DIFFRACTION24chain 'H' and (resid 98 through 117 )H98 - 117
25X-RAY DIFFRACTION25chain 'H' and (resid 118 through 148 )H118 - 148
26X-RAY DIFFRACTION26chain 'H' and (resid 149 through 156 )H149 - 156
27X-RAY DIFFRACTION27chain 'H' and (resid 157 through 175 )H157 - 175
28X-RAY DIFFRACTION28chain 'H' and (resid 176 through 192 )H176 - 192
29X-RAY DIFFRACTION29chain 'H' and (resid 193 through 215 )H193 - 215
30X-RAY DIFFRACTION30chain 'H' and (resid 216 through 228 )H216 - 228
31X-RAY DIFFRACTION31chain 'H' and (resid 229 through 248 )H229 - 248
32X-RAY DIFFRACTION32chain 'H' and (resid 249 through 259 )H249 - 259

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