[English] 日本語
Yorodumi
- PDB-8pxe: Crystal structure of the N-terminal dimerisation domain of Hh1141 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pxe
TitleCrystal structure of the N-terminal dimerisation domain of Hh1141
ComponentsDisulfide isomerase DsbG N-terminal domain-containing protein
KeywordsOXIDOREDUCTASE / disulfide bonds / Dsb
Function / homologyDisulfide isomerase DsbG, N-terminal / Disulfide isomerase DsbG N-terminal / Thioredoxin-like superfamily / Disulfide isomerase DsbG N-terminal domain-containing protein
Function and homology information
Biological speciesHelicobacter hepaticus ATCC 51449 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsWilk, P. / Roszczenko-Jasinska, P. / Jagusztyn-Krynicka, E.K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2018/29/B/NZ1/00140 Poland
CitationJournal: To Be Published
Title: Crystal structures of Disulfide oxidoreductase/isomerase from Helicobacter hepaticus.
Authors: Roszczenko-Jasinska, P.
History
DepositionJul 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Disulfide isomerase DsbG N-terminal domain-containing protein
B: Disulfide isomerase DsbG N-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)53,6302
Polymers53,6302
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-19 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.004, 66.004, 113.245
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASNASN(chain 'A' and (resid 2 through 16 or resid 18 through 20 or resid 22 through 79 or resid 81))AA2 - 152 - 15
12GLNGLNASPASP(chain 'A' and (resid 2 through 16 or resid 18 through 20 or resid 22 through 79 or resid 81))AA18 - 1918 - 19
13ILEILELEULEU(chain 'A' and (resid 2 through 16 or resid 18 through 20 or resid 22 through 79 or resid 81))AA22 - 7822 - 78
24ALAALAASNASN(chain 'B' and (resid 2 through 16 or resid 18 through 20 or resid 22 through 79 or resid 81))BB2 - 152 - 15
25GLNGLNASPASP(chain 'B' and (resid 2 through 16 or resid 18 through 20 or resid 22 through 79 or resid 81))BB18 - 1918 - 19
26ILEILELEULEU(chain 'B' and (resid 2 through 16 or resid 18 through 20 or resid 22 through 79 or resid 81))BB22 - 7822 - 78

-
Components

#1: Protein Disulfide isomerase DsbG N-terminal domain-containing protein


Mass: 26815.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Appears to be proteolytically cleaved in the crystallization drop.
Source: (gene. exp.) Helicobacter hepaticus ATCC 51449 (bacteria)
Gene: HH_1141 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): (DE3) LacIq / References: UniProt: Q7VH26

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PACT F8 | 0.2 M sodium sulfate, 0.1 M Bis Tris propane 6.5, 20 % w/v PEG 3350. 30% EDO used as cryoprotectant.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2021 / Details: Elliptically bent mirror
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.23→46.67 Å / Num. obs: 4360 / % possible obs: 99.8 % / Redundancy: 12.14 % / Biso Wilson estimate: 112.27 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.17 / Rrim(I) all: 0.178 / Net I/σ(I): 14.75
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.23-3.431.7326750.6111.8041
3.43-3.661.0636440.8321.1091
3.66-3.960.5935940.960.6191
3.96-4.330.3025580.990.3151
4.33-4.840.1475050.9950.1541
4.84-5.570.1294560.9970.1351
5.57-6.80.1043970.9970.1091
6.8-9.520.0663250.9980.0691
9.52-46.670.0452050.9970.0481

-
Processing

Software
NameVersionClassification
PHENIX1.15.1_3469refinement
XDSdata scaling
PHASERphasing
XDSdata reduction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.23→46.67 Å / SU ML: 0.4243 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.4314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2448 218 5 %
Rwork0.1839 4142 -
obs0.187 4360 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.62 Å2
Refinement stepCycle: LAST / Resolution: 3.23→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 0 0 1224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01421236
X-RAY DIFFRACTIONf_angle_d1.66411658
X-RAY DIFFRACTIONf_chiral_restr0.0819203
X-RAY DIFFRACTIONf_plane_restr0.0082207
X-RAY DIFFRACTIONf_dihedral_angle_d3.0319770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.23-4.070.32421050.24082000X-RAY DIFFRACTION99.53
4.07-46.670.21691130.16462142X-RAY DIFFRACTION100
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)
10.128280494505-0.3727581103210.2597215224041.0846688333-0.7550429756890.528031399343-0.188881588702-0.492886719588-0.885977868970.9882349892390.4972316777321.12883816468-1.066871747640.4661184277880.06800340596720.948934202863-0.0181883297975-0.1368954468190.768861457526-0.180392255611.10127309257-9.8808652103327.658251722428.5911995703
20.2685256045490.09936693577060.2384127033370.04014264379250.101275237690.239027460129-0.396118173607-0.425114421757-0.9836967911460.09810924578180.2851660078010.779392538310.02513704520550.1392579536830.001669146605990.729697313269-0.008045687132960.02534428681950.934021325339-0.01101016525120.982768801654-6.0164906717421.110173823431.8349673786
31.12717968113-0.4912420837050.8925734682020.5773599277880.0194899358931.1603054050.1210343009180.0114228212136-0.161471984679-0.2291736607460.0604612842483-0.245984103064-0.3286808085890.378419690934-0.0008126632241630.7144831640570.08401312449440.07071496033350.8716188233750.01809787593830.724483807359-1.3370752214520.409976868420.8192370235
40.6398745181860.0394172269070.4572031911150.2196917580260.1896869496510.446945681331-0.690773477432-0.7531424404290.006054461676090.6999338443180.2825745054690.0216977581791-0.36925974074-0.249374042679-0.1370167432231.277928697170.833617472850.01944824058181.324724695430.5122994544541.884329593276.0887787447512.919554662420.7428001186
51.51807108590.4180903224880.6238900692930.57765965422-0.3988517624440.926085789940.03399670747730.2399762891570.354752034718-0.323217728550.0321102161486-0.0996356340064-0.2040340995350.6225268337460.0002354927934530.9378240487540.1180716404330.04129935003590.877852553722-0.03888610866390.690863702835-4.2145583455621.93588499116.74948834155
60.15264334444-0.2105386563410.2474997343232.07489745942-2.305261510522.56247691264-0.3476907772460.882397738753-1.1585546174-1.583067229720.4426002784260.3390421622361.481695827360.653638118620.06583631257831.09691964297-0.055975248761-0.07628347269581.07677553591-0.2065177109641.58025711831-17.376044354320.81534810169.57600892988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 26 )
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 81 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 68 )
6X-RAY DIFFRACTION6chain 'B' and (resid 69 through 83 )

+
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