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- PDB-6nen: Catalytic domain of Proteus mirabilis ScsC -

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Basic information

Entry
Database: PDB / ID: 6nen
TitleCatalytic domain of Proteus mirabilis ScsC
ComponentsCopper resistance protein
KeywordsOXIDOREDUCTASE / Disulfide bond / Isomerase / Copper
Function / homology
Function and homology information


disulfide oxidoreductase activity
Similarity search - Function
Copper resistance protein ScsC, N-terminal / Copper resistance protein ScsC N-terminal domain / Thioredoxin / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Copper resistance protein / Putative metal resistance protein
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsKurth, F. / Furlong, E.J. / Premkumar, L. / Martin, J.L.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FL0992138, J.L.M. Australia
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Engineered variants provide new insight into the structural properties important for activity of the highly dynamic, trimeric protein disulfide isomerase ScsC from Proteus mirabilis.
Authors: Furlong, E.J. / Kurth, F. / Premkumar, L. / Whitten, A.E. / Martin, J.L.
History
DepositionDec 17, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMar 6, 2019ID: 4YX8
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper resistance protein


Theoretical massNumber of molelcules
Total (without water)20,1771
Polymers20,1771
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.501, 105.501, 35.132
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312

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Components

#1: Protein Copper resistance protein / DsbA family protein / Metal resistance protein


Mass: 20177.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: bdbD, AM402_16750, C6A90_15705, NCTC10975_02509 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) pLysS / References: UniProt: A0A1Z1SYD5, UniProt: B4EV21*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Sodium acetate trihydrate, 30% w/v PEG-mono methylether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.15→45.68 Å / Num. obs: 12203 / % possible obs: 99.7 % / Redundancy: 21.8 % / Biso Wilson estimate: 28.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.029 / Rrim(I) all: 0.135 / Net I/σ(I): 21.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.15-2.2220.50.87710270.9190.1940.89997
8.86-45.68190.0371830.9990.0090.03897.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.24data extraction
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GXZ

4gxz


Resolution: 2.151→35.132 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 22.97
RfactorNum. reflection% reflection
Rfree0.2077 581 4.76 %
Rwork0.1752 --
obs0.1768 12196 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.16 Å2 / Biso mean: 38.1075 Å2 / Biso min: 14.02 Å2
Refinement stepCycle: final / Resolution: 2.151→35.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 0 68 1401
Biso mean---37.23 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041355
X-RAY DIFFRACTIONf_angle_d0.8151840
X-RAY DIFFRACTIONf_chiral_restr0.031221
X-RAY DIFFRACTIONf_plane_restr0.005235
X-RAY DIFFRACTIONf_dihedral_angle_d12.995501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1506-2.3670.25361560.20572859301599
2.367-2.70940.22971360.188429043040100
2.7094-3.41310.23911440.196228893033100
3.4131-35.13670.17361450.152929633108100

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