[English] 日本語
Yorodumi
- PDB-8eoc: Crystal structure of E.coli DsbA mutant E24A/K58A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8eoc
TitleCrystal structure of E.coli DsbA mutant E24A/K58A
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / DsbA mutant / thioredoxin-family protein
Function / homology
Function and homology information


cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space
Similarity search - Function
Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
COPPER (II) ION / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsWang, G. / Heras, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1144046 Australia
CitationJournal: Antioxidants / Year: 2023
Title: A Buried Water Network Modulates the Activity of the Escherichia coli Disulphide Catalyst DsbA.
Authors: Wang, G. / Qin, J. / Verderosa, A.D. / Hor, L. / Santos-Martin, C. / Paxman, J.J. / Martin, J.L. / Totsika, M. / Heras, B.
History
DepositionOct 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thiol:disulfide interchange protein DsbA
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3265
Polymers42,0782
Non-polymers2483
Water6,359353
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1312
Polymers21,0391
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1953
Polymers21,0391
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.013, 63.590, 74.716
Angle α, β, γ (deg.)90.000, 126.770, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

-
Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21038.887 Da / Num. of mol.: 2 / Mutation: E24A, K58A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEG4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 11-13% PEG 8000, 5-7.5% glycerol, 1 mM copper(II) chloride, 100 mM sodium cacodylate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.47→48.41 Å / Num. obs: 74603 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.028 / Rrim(I) all: 0.056 / Net I/σ(I): 11.2 / Num. measured all: 279376 / Scaling rejects: 17
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
1.47-1.493.60.7671175932630.6610.4540.8941.487.6
8.04-48.413.50.03216534700.9970.0190.03828.794.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.47→37.32 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1967 3784 5.07 %
Rwork0.1762 70800 -
obs0.1773 74584 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.77 Å2 / Biso mean: 33.1846 Å2 / Biso min: 15.41 Å2
Refinement stepCycle: final / Resolution: 1.47→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 29 353 3322
Biso mean--65.05 39.24 -
Num. residues----376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.490.34181210.30242234235584
1.49-1.510.31651510.263626312782100
1.51-1.530.26221530.257826302783100
1.53-1.550.26361670.243926072774100
1.55-1.570.29091520.223826382790100
1.57-1.60.21411560.213526422798100
1.6-1.620.25441440.221326512795100
1.62-1.650.24881460.216226432789100
1.65-1.680.25721230.220926462769100
1.68-1.710.23871350.216126442779100
1.71-1.750.25661360.209526572793100
1.75-1.790.22241210.196826612782100
1.79-1.830.22061130.185426972810100
1.83-1.870.2111320.191426732805100
1.87-1.920.24571330.184326572790100
1.92-1.980.18351240.19442618274299
1.98-2.040.21091400.19352643278399
2.04-2.120.1951570.18632599275699
2.12-2.20.19921590.17842616277599
2.2-2.30.20581140.1792632274698
2.3-2.420.20791310.1822610274198
2.42-2.580.23781340.18812636277098
2.58-2.770.20161340.17272602273697
2.77-3.050.21331620.17632584274698
3.05-3.490.15221220.16262624274698
3.49-4.40.15541730.14252627280098
4.4-37.320.18971510.16372698284998
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6710.19110.5542.292.1842.28080.16450.1360.0378-0.9024-0.26820.6792-0.4329-0.03890.06640.49770.053-0.10120.2783-0.07990.35925.3379-13.3418-13.7878
23.19513.23940.24479.6377-2.59682.4522-0.32770.45260.3306-0.7224-0.2791-0.9202-0.58430.73620.36040.443-0.05230.0990.5327-0.04670.29838.3433-3.1063-9.2371
32.59540.1225-0.60362.34361.10383.6603-0.03740.1438-0.1713-0.08280.01510.14670.0428-0.09540.06030.2023-0.0366-0.00320.1618-0.01330.16726.8432-7.13257.9032
44.8437-0.3138-2.33152.80971.51396.1122-0.3334-0.1166-0.54560.1304-0.0509-0.06770.89620.50910.04190.34830.02910.01340.2521-0.01580.306730.1209-18.64385.1481
52.2699-0.0261-0.56554.85472.46764.7296-0.1440.2028-0.3353-0.18720.3032-0.20360.11080.6018-0.10950.2094-0.0278-0.00960.3082-0.04310.272135.8583-7.52683.4787
64.10520.3780.37991.76570.18482.7022-0.058-0.0355-0.04850.06080.0718-0.01120.04520.1383-0.02050.1826-0.0321-0.01580.17210.00020.150432.9268-3.412418.6798
74.81383.6617-1.65579.5477-3.14095.3072-0.1688-0.2784-0.28930.3248-0.0258-0.56830.01050.68350.1750.19260.0051-0.03820.299-0.00060.213544.1895-1.724622.8958
82.2016-0.62832.59790.96-0.28564.223-0.13850.51420.2372-0.25480.1636-0.1956-0.27410.49890.02370.2826-0.17020.03750.4255-0.01690.206842.23093.11885.5672
93.60581.3412-2.20414.71690.89068.0657-0.07050.4147-0.0011-0.72970.0524-0.0243-0.33950.14690.0320.2782-0.0582-0.00120.2962-0.01560.170231.2679-4.5895-5.2392
103.17671.4630.31687.3942-3.55846.7891-0.47280.3959-0.0488-0.36580.2551.70320.5006-1.430.02990.3917-0.0755-0.00470.5187-0.13120.521818.4188-14.5283-4.4374
118.0343-0.8413-4.63794.08871.29526.862-0.50750.0831-0.4910.0055-0.07830.52770.7459-0.21050.62350.34280.01530.01750.2366-0.11440.270528.038-18.448-4.8091
1222-1.19772-2.71982-0.3216-1.28453.70491.49470.1082-2.8588-0.56731.17760.21490.6996-0.01080.11780.2797-0.04940.689532.3413-10.34488.8219
134.74951.92221.79593.89810.67716.13220.22810.39560.3599-0.54510.00030.6908-1.0167-0.6987-0.11840.5030.19750.02160.39320.03780.44061.84449.251120.3534
141.55460.3084-0.15382.67191.35373.7008-0.0073-0.0092-0.0040.00170.0810.0256-0.0891-0.1688-0.07630.1873-0.02570.00220.18190.01640.210410.5339-9.03819.0882
155.8002-1.4295-2.51353.70082.19364.6234-0.116-0.1923-0.24510.4807-0.0430.5640.3797-0.13310.04610.3132-0.02360.09530.20720.0070.33726.6532-6.529330.507
161.6067-0.4564-0.5463.70891.82974.65240.1649-0.03540.4463-0.1448-0.170.5723-0.2245-0.62810.0850.1912-0.0310.00860.38290.01740.38610.8171-6.648318.7552
176.27581.6386-0.98574.81910.46071.2434-0.19220.6690.169-0.65310.16450.3604-0.0517-0.28370.06770.2624-0.0726-0.07320.28160.0070.21432.9884-17.350410.8006
184.72851.809-1.85134.2055-0.0482.0292-0.1312-0.0372-0.5027-0.0714-0.056-0.40.14850.00220.16450.2171-0.04440.00210.21460.01140.253810.2142-22.804216.3845
196.10410.16673.15852.5954-0.39217.4054-0.36380.3753-0.4305-0.41060.31560.23580.5118-0.74360.0480.2484-0.15430.01590.3876-0.02620.2374-2.1907-27.803511.9908
201.80471.8148-0.01174.89740.48442.5081-0.08980.18610.5555-0.8010.03751.03-0.0198-0.76340.06390.3847-0.0032-0.18070.51370.11870.4274-4.5729-10.08628.3953
213.5542-0.40051.26545.83060.70692.9326-0.00270.01810.401-0.46450.0630.7325-0.9445-0.7636-0.03540.31910.1168-0.01860.27990.07250.34583.48892.477715.7773
222.2425-0.82090.45666.6182-5.04276.46250.03450.09330.2139-0.3979-0.1586-0.8301-0.63921.04010.01990.4022-0.05930.22940.3275-0.04250.50515.47554.887126.4799
234.58350.77721.77954.4608-0.40346.80540.1522-0.19790.650.0956-0.10310.2337-0.2081-0.3409-0.11420.30720.02230.1280.1801-0.01340.35325.72443.351730.1018
247.86064.22811.77272.32580.95350.3998-1.99211.91382.3901-9.77161.87425.982-1.4378-1.28850.2170.8349-0.0109-0.1560.97920.14780.75336.1506-11.667621.3234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )A1 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 21 )A12 - 21
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 38 )A22 - 38
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 49 )A39 - 49
5X-RAY DIFFRACTION5chain 'A' and (resid 50 through 65 )A50 - 65
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 114 )A66 - 114
7X-RAY DIFFRACTION7chain 'A' and (resid 115 through 128 )A115 - 128
8X-RAY DIFFRACTION8chain 'A' and (resid 129 through 144 )A129 - 144
9X-RAY DIFFRACTION9chain 'A' and (resid 145 through 161 )A145 - 161
10X-RAY DIFFRACTION10chain 'A' and (resid 162 through 170 )A162 - 170
11X-RAY DIFFRACTION11chain 'A' and (resid 171 through 188 )A171 - 188
12X-RAY DIFFRACTION12chain 'A' and (resid 201 through 201 )A201
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 21 )B1 - 21
14X-RAY DIFFRACTION14chain 'B' and (resid 22 through 38 )B22 - 38
15X-RAY DIFFRACTION15chain 'B' and (resid 39 through 49 )B39 - 49
16X-RAY DIFFRACTION16chain 'B' and (resid 50 through 65 )B50 - 65
17X-RAY DIFFRACTION17chain 'B' and (resid 66 through 82 )B66 - 82
18X-RAY DIFFRACTION18chain 'B' and (resid 83 through 114 )B83 - 114
19X-RAY DIFFRACTION19chain 'B' and (resid 115 through 128 )B115 - 128
20X-RAY DIFFRACTION20chain 'B' and (resid 129 through 144 )B129 - 144
21X-RAY DIFFRACTION21chain 'B' and (resid 145 through 161 )B145 - 161
22X-RAY DIFFRACTION22chain 'B' and (resid 162 through 170 )B162 - 170
23X-RAY DIFFRACTION23chain 'B' and (resid 171 through 188 )B171 - 188
24X-RAY DIFFRACTION24chain 'B' and (resid 201 through 201 )B201

+
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