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- PDB-8pxf: Crystal structure of the full length Hh1412 Dsb homodimer. -

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Basic information

Entry
Database: PDB / ID: 8pxf
TitleCrystal structure of the full length Hh1412 Dsb homodimer.
ComponentsDisulfide bond oxidoreductase/isomerase
KeywordsOXIDOREDUCTASE / disulfide bond formation / Dsb
Function / homologyThioredoxin-like superfamily / Uncharacterized protein
Function and homology information
Biological speciesHelicobacter hepaticus ATCC 51449 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsWilk, P. / Orlikowska, M. / 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 bond oxidoreductase/isomerase
B: Disulfide bond oxidoreductase/isomerase


Theoretical massNumber of molelcules
Total (without water)48,7022
Polymers48,7022
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-17 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.260, 87.260, 130.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Disulfide bond oxidoreductase/isomerase


Mass: 24351.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter hepaticus ATCC 51449 (bacteria)
Gene: HH_1412 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3) LacIq / References: UniProt: Q7VGB0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Morpheus A4; 0.06 M Divalents, 0.1 M Buffer System 1 6.5, 50 % v/v Precipitant Mix 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.13→44.84 Å / Num. obs: 28892 / % possible obs: 100 % / Redundancy: 11.45 % / Biso Wilson estimate: 71.51 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.126 / Net I/σ(I): 9.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.13-2.2611.971.8141.0145640.5271.895100
2.26-2.411.00543180.7821.05
2.41-2.610.50340330.9310.528
2.61-2.860.26337160.9770.276
2.86-3.190.15733740.9880.165
3.19-3.680.12130230.9930.126
3.68-4.50.10625880.9910.111
4.5-6.330.10320420.9920.108
6.33-44.840.10812340.9880.114

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→43.63 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2641 1445 5 %
Rwork0.2301 --
obs0.2318 28890 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 0 36 3370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.566
X-RAY DIFFRACTIONf_dihedral_angle_d17.9631296
X-RAY DIFFRACTIONf_chiral_restr0.093520
X-RAY DIFFRACTIONf_plane_restr0.008584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.210.42951410.39122680X-RAY DIFFRACTION100
2.21-2.290.35691420.34532707X-RAY DIFFRACTION100
2.29-2.40.32821420.30192681X-RAY DIFFRACTION100
2.4-2.530.33751420.29052701X-RAY DIFFRACTION100
2.53-2.680.37461430.29442715X-RAY DIFFRACTION100
2.68-2.890.36371430.30582718X-RAY DIFFRACTION100
2.89-3.180.33921440.27012733X-RAY DIFFRACTION100
3.18-3.640.28181460.2442774X-RAY DIFFRACTION100
3.64-4.590.22271460.19562787X-RAY DIFFRACTION100
4.59-43.630.22461560.19982949X-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)
10.4514-0.5545-1.57163.16791.95953.6567-0.1858-0.0233-0.16150.30270.1294-0.24450.13920.26760.10430.5234-0.0273-0.03230.5842-0.07720.745325.043228.842523.8613
26.6606-0.31021.12462.4598-0.24895.2853-0.0226-0.0650.0239-0.0734-0.04030.2091-0.1819-0.43910.07320.69570.0280.00130.4148-0.02990.37532.806338.412644.5038
34.3722-1.55665.15163.16571.11989.36230.12860.7092-1.7748-0.21981.057-0.56690.41130.9744-1.16020.85310.10460.16190.7444-0.15971.121329.14233.835314.0028
44.65182.38831.52273.76572.34631.564-1.10990.0689-1.2841-0.18911.24210.6251.19740.25060.08760.82340.08460.42110.756-0.03331.126722.9437.024811.235
53.09082.21222.50835.675-0.03483.0857-0.2382-0.24340.2436-0.17080.35740.4851-0.202-0.2517-0.12860.59930.02110.07760.5773-0.03720.799320.350812.623612.2145
64.81827.43970.42078.30610.60431.0159-0.46540.27950.3301-0.4650.4120.6346-0.3490.1908-0.02710.58720.00570.01780.6238-0.00260.75017.00978.13215.2204
76.1446-1.228-0.46673.6777-0.6015.6897-0.1341-0.74850.50.46520.20240.0333-0.4248-0.3826-0.12880.52370.07320.05120.7265-0.06330.7326-13.5394-1.545413.0914
85.795-0.3478-1.91492.3056-0.57082.1754-0.6322-1.7637-0.3890.78760.43870.03740.0350.18730.24340.72910.18830.04191.17950.1560.7135-11.2612-11.236421.3909
95.1829-0.024-0.66087.3793-2.54324.34020.55980.4434-0.4790.00180.02421.423-0.0676-0.3487-0.46990.5983-0.0442-0.08010.6922-0.18230.8805-4.26144.24189.3982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 213 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 12 )
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 28 )
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 62 )
6X-RAY DIFFRACTION6chain 'B' and (resid 63 through 94 )
7X-RAY DIFFRACTION7chain 'B' and (resid 95 through 148 )
8X-RAY DIFFRACTION8chain 'B' and (resid 149 through 201 )
9X-RAY DIFFRACTION9chain 'B' and (resid 202 through 215 )

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