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- PDB-8pxd: Crystal structure of the C-terminal domain of Hh1412 -

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Basic information

Entry
Database: PDB / ID: 8pxd
TitleCrystal structure of the C-terminal domain of Hh1412
ComponentsDisulfide bond oxidoreductase/isomerase - Dsb
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: 2.2 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 - Dsb


Theoretical massNumber of molelcules
Total (without water)24,3511
Polymers24,3511
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.700, 64.480, 119.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Disulfide bond oxidoreductase/isomerase - Dsb


Mass: 24351.004 Da / Num. of mol.: 1
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_1412 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): (DE3) LacIq / References: UniProt: Q7VGB0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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

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: 2.09→35.96 Å / Num. obs: 8910 / % possible obs: 99.6 % / Redundancy: 12.38 % / CC1/2: 0.993 / Rmerge(I) obs: 0.21 / Rrim(I) all: 0.219 / Net I/σ(I): 6.41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.09-2.2211.851.3241.1313780.8521.38397.6
2.22-2.370.96713210.881.012
2.37-2.560.54912400.9730.572
2.56-2.810.39211500.9760.408
2.81-3.130.26910520.9860.28
3.13-3.610.2039300.9870.212
3.61-4.420.1758050.9870.182
4.42-6.20.1616410.9860.168
6.2-35.960.1433930.9920.149

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Processing

Software
NameVersionClassification
PHENIX(1.15.1_3469: ???)refinement
XDSdata scaling
MoRDaphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→35.954 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 387 5.02 %
Rwork0.1914 --
obs0.1944 7715 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→35.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 0 71 1099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171046
X-RAY DIFFRACTIONf_angle_d1.0611404
X-RAY DIFFRACTIONf_dihedral_angle_d8.017660
X-RAY DIFFRACTIONf_chiral_restr0.054162
X-RAY DIFFRACTIONf_plane_restr0.004178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27870.4393370.2922703X-RAY DIFFRACTION99
2.2787-2.36990.2802280.2412712X-RAY DIFFRACTION100
2.3699-2.47770.2639380.2157717X-RAY DIFFRACTION100
2.4777-2.60830.3276380.2335722X-RAY DIFFRACTION99
2.6083-2.77170.2152380.2342721X-RAY DIFFRACTION100
2.7717-2.98560.3343380.223724X-RAY DIFFRACTION100
2.9856-3.28580.2688390.2057730X-RAY DIFFRACTION100
3.2858-3.76090.2659390.1772743X-RAY DIFFRACTION100
3.7609-4.73660.1593390.1513755X-RAY DIFFRACTION100
4.7366-35.9540.2701430.177801X-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)
11.79161.1184-0.52330.7907-0.28270.59770.1058-0.06660.1306-0.13760.01630.0487-0.21270.34790.00040.43620.0686-0.03840.4479-0.01510.401533.294618.80139.2509
20.05140.1468-0.10760.331-0.22630.2604-0.1003-0.11610.41120.0498-0.27930.1467-0.72410.8455-0.02410.58360.0539-0.02360.588-0.07850.457534.240122.285153.5768
30.91080.69250.81431.66720.13640.8571-0.0776-0.81890.09550.1481-0.11320.21710.01-0.2393-0.32860.43940.01690.13320.74070.04730.354922.984810.797350.8811
41.81980.00330.06691.45750.13830.49680.049-0.00950.0842-0.0098-0.08410.09840.07860.05630.00010.3587-0.0390.0020.42140.04760.357629.714610.573440.6891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 177 through 212 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 110 )
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 176 )

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