[English] 日本語
Yorodumi
- PDB-6pbi: Crystal Structure of EcDsbA in a complex with purified morpholine 8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pbi
TitleCrystal Structure of EcDsbA in a complex with purified morpholine 8
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / DSBA / OXIDOREDUCTASE-INHIBITOR COMPLEX / REFiLX / OXIDOREDUCTASE
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 / Glutaredoxin / Glutaredoxin ...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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Chem-O6Y / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsIlyichova, O.V. / Bentley, M. / Doak, B. / Scanlon, M.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)Project Grant APP1099151 Australia
Australian Research Council (ARC)LIEF LE160100047 Australia
CitationJournal: J.Med.Chem. / Year: 2020
Title: Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiL X ).
Authors: Bentley, M.R. / Ilyichova, O.V. / Wang, G. / Williams, M.L. / Sharma, G. / Alwan, W.S. / Whitehouse, R.L. / Mohanty, B. / Scammells, P.J. / Heras, B. / Martin, J.L. / Totsika, M. / Capuano, ...Authors: Bentley, M.R. / Ilyichova, O.V. / Wang, G. / Williams, M.L. / Sharma, G. / Alwan, W.S. / Whitehouse, R.L. / Mohanty, B. / Scammells, P.J. / Heras, B. / Martin, J.L. / Totsika, M. / Capuano, B. / Doak, B.C. / Scanlon, M.J.
History
DepositionJun 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 11, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
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)42,7104
Polymers42,3102
Non-polymers4002
Water5,513306
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4912
Polymers21,1551
Non-polymers3361
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)21,2192
Polymers21,1551
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.734, 64.624, 74.404
Angle α, β, γ (deg.)90.000, 125.783, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-447-

HOH

-
Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21155.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Plasmid: B0013 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEG4
#2: Chemical ChemComp-O6Y / 2-methyl-4-{4-[2-(morpholin-4-yl)-2-oxoethyl]phenoxy}benzonitrile


Mass: 336.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 25-35 % PEG MME 2000, 100-300 mM KBr

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 21, 2018
RadiationMonochromator: DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→34.79 Å / Num. obs: 35587 / % possible obs: 99.2 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.036 / Rrim(I) all: 0.054 / Χ2: 1 / Net I/σ(I): 17.1
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2191 / CC1/2: 0.753 / Rpim(I) all: 0.517 / Rrim(I) all: 0.789 / Χ2: 0.98 / % possible all: 96

-
Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
XDSdata reduction
Aimless1.11.12data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DSB

1dsb


Resolution: 1.9→34.79 Å / SU ML: 0.2294 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8154
RfactorNum. reflection% reflection
Rfree0.2283 1737 4.88 %
Rwork0.1905 --
obs0.1924 35578 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 26 306 3202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683010
X-RAY DIFFRACTIONf_angle_d0.79784099
X-RAY DIFFRACTIONf_chiral_restr0.0441449
X-RAY DIFFRACTIONf_plane_restr0.0049539
X-RAY DIFFRACTIONf_dihedral_angle_d6.0832707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.31031180.27882792X-RAY DIFFRACTION97.36
1.96-2.020.27971410.25212821X-RAY DIFFRACTION99.93
2.02-2.090.27531470.24032803X-RAY DIFFRACTION99.9
2.09-2.170.30561370.2242834X-RAY DIFFRACTION99.93
2.17-2.270.26041550.21382807X-RAY DIFFRACTION100
2.27-2.390.27481540.21192844X-RAY DIFFRACTION100
2.39-2.540.28721710.21062763X-RAY DIFFRACTION99.83
2.54-2.740.28081320.21682873X-RAY DIFFRACTION99.9
2.74-3.010.2481220.20262858X-RAY DIFFRACTION99.73
3.01-3.450.21881590.19242802X-RAY DIFFRACTION98.8
3.45-4.350.19081400.15662788X-RAY DIFFRACTION97.31
4.35-34.790.18091610.1612856X-RAY DIFFRACTION97.86
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)
11.55656565173-0.3645127384330.9630815058472.463429962491.753576333372.175493676490.07423133256540.311993638152-0.050067466905-0.319197831118-0.01630623386090.116613508657-0.0518215373230.145438308873-0.008446198011890.280641436492-0.021596949224-0.0314217283130.20264334634-0.01993534053720.19187500868629.1256378704-7.38718411961-1.6943176593
29.39022379667-2.88451693092-4.81529399445.31528577681.383504855587.790276049960.160821483256-0.484347930001-0.5346023475720.495524053907-0.08960995958280.001698133447280.3562450249690.4645535318020.01990300134450.32940322565-0.0465399961146-0.0377931159360.250521128526-0.006664184109780.22388245560430.946322724-18.00029343945.62767587801
31.329589072071.519185815980.4193125240724.114886353841.85513619513.73785413306-0.1548252053120.15876912653-0.470978904625-0.2292443845860.331469073212-0.4301363728410.2046380729660.433083643578-0.175759243420.1871082124950.003762525509570.01247511126570.218703271759-0.05707905496630.3018292803835.9070826808-6.183498692754.29348261033
42.209467123340.7800265678410.1177894094322.157122076960.1835293807883.34349262139-0.0375231409397-0.1247361046780.07323574370040.081674637417-0.00828466193507-0.1411801291510.1925520189890.311552927340.04073657021580.2100274942840.0243323211843-0.03165921857450.221721134333-0.004570484298610.21490609334737.1879494165-0.27399216116516.7069121078
53.891992125610.351151903412-0.6011363464546.23244327741.681021698375.95208504242-0.2209838943470.6386322541460.0951539550082-0.8560490119470.3647500431010.0178283160232-0.261414723804-0.0114693640922-0.09346851946290.270366410541-0.0822553560902-0.02368026576220.3127045272790.007709574864950.21459718332231.2016355812-4.99256841855-4.20405208452
62.573915857490.974678081423-0.8267282686532.25436472882-0.8943942954592.45959969974-0.08482401669830.07500424380570.009397866364630.06566139276470.1217827849610.0255778293759-0.0586803783901-0.123250484787-0.05439971320820.3021403384480.0279817252561-0.05212765742710.215553392738-0.04400820710960.22657467046724.6183011457-17.1967940868-2.84983796392
71.2583587017-0.618794835664-0.8937529720781.49007365684-0.1709983852280.9417406558830.6886644529320.5694362943680.413217707332-1.09315257-0.3379999855280.0806619522184-0.861213471178-0.582202296382-0.02020596434711.149919856750.5227363563030.3107121325260.7374215406980.04543018867810.7097478834382.5867833674610.435291698920.6470446522
81.160707832690.6621039999330.8774715933782.700406770261.675292340854.275730823050.09339402795150.1668697642080.2298064051820.0298304533319-0.2181458704880.437824480744-0.0864219461454-0.592002810480.0240238638250.318300315210.01586364705020.05637680760290.337486464119-0.02908746205710.3648944015996.90168357321-6.5886481346821.6619209535
93.488170667120.65818027875-1.167029084482.020811240150.0577674716661.42515665511-0.00654038182289-0.171803652268-0.142612848346-0.0827549281374-0.1025432880460.174609161704-0.028853313764-0.1890161718570.105473321940.253321912029-0.041802585468-0.01783872189210.374346701751-0.004408003213350.2964773284076.34380467386-21.405555206714.248033569
101.502963931020.2742730879991.312091312523.824546451541.730270739873.034796879760.101567715342-0.05083704062890.670923647822-0.700106368127-0.2036782683990.718294590356-0.919562062546-0.8078990089080.1373151540090.6682482502890.2791790061120.04756846085680.6876256704060.09912968752790.5393658464680.264002669331-2.7746653916812.4588936066
112.252239686930.00594075204324-0.047762941264.61637732415-4.371618974836.294380325290.4476401180660.3641561951060.0735513839531-0.603016807108-0.359794766677-0.417336915164-0.4260616649590.6801206055150.01061742919580.9077361004110.1100517142050.4039819565780.3830905336340.008981444047490.62649860962815.80212561546.2424096005426.6270371204
125.200183344010.8018510581841.409939352823.81011025546-0.5407874947684.327055023970.4821967985630.1899129496360.422157910139-0.185144001549-0.396280539350.301755728103-0.710572510772-0.5928288857160.01664782148240.5098437969840.1442198122420.2179234704720.374273052194-0.06327080289870.5239992095525.964675793274.8211823928430.014773174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 145 )
5X-RAY DIFFRACTION5chain 'A' and (resid 146 through 161 )
6X-RAY DIFFRACTION6chain 'A' and (resid 162 through 188 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 21 )
8X-RAY DIFFRACTION8chain 'B' and (resid 22 through 65 )
9X-RAY DIFFRACTION9chain 'B' and (resid 66 through 128 )
10X-RAY DIFFRACTION10chain 'B' and (resid 129 through 161 )
11X-RAY DIFFRACTION11chain 'B' and (resid 162 through 170 )
12X-RAY DIFFRACTION12chain 'B' and (resid 171 through 188 )

+
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