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- PDB-8pxe: Crystal structure of the N-terminal dimerisation domain of Hh1141 -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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

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.

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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

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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 )

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