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- PDB-5id4: Crystal structure of Proteus mirabilis ScsC in an extended confor... -

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Basic information

Entry
Database: PDB / ID: 5id4
TitleCrystal structure of Proteus mirabilis ScsC in an extended conformation
ComponentsDsbA-like protein
KeywordsISOMERASE / thioredoxin fold / disulfide isomerase / trimer / copper resistance
Function / homology:
Function and homology information
Biological speciesProteus mirabilis ATCC 29906 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.921 Å
AuthorsFurlong, E.J. / Kurth, F. / Choudhury, H.G. / Martin, J.L.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FL0992138 Australia
CitationJournal: Nat Commun / Year: 2017
Title: Proteus mirabilis ScsC is a highly dynamic, novel trimeric protein disulfide isomerase
Authors: Kurth, F. / Furlong, E.J. / Lo, A.W. / Premkumar, L. / Totsika, M. / Whitten, A.E. / Achard, M.E.S. / Halili, M.A. / Heras, B. / Choudhury, H.G. / Schembri, M.A. / Martin, J.L.
History
DepositionFeb 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DsbA-like protein


Theoretical massNumber of molelcules
Total (without water)24,8001
Polymers24,8001
Non-polymers00
Water00
1
A: DsbA-like protein

A: DsbA-like protein

A: DsbA-like protein


Theoretical massNumber of molelcules
Total (without water)74,4013
Polymers74,4013
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area4600 Å2
ΔGint-37 kcal/mol
Surface area35730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.745, 86.745, 330.858
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein DsbA-like protein


Mass: 24800.443 Da / Num. of mol.: 1 / Fragment: UNP residues 22-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis ATCC 29906 (bacteria)
Gene: HMPREF0693_3732 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: C2LPE2
Has protein modificationY

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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: 4.83 Å3/Da / Density % sol: 74.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 32% Jeffamine M-600 pH 7, 0.1 M HEPES pH 8, 2.5 mM Copper(II) chloride
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.92→110.29 Å / Num. obs: 10755 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 85.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.033 / Rrim(I) all: 0.068 / Net I/σ(I): 14.2 / Num. measured all: 44513
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.92-3.084.30.554660615360.970.3020.6322.899.8
9.24-110.293.40.03812003570.9970.0220.04433.691.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.8data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YX8

4yx8
PDB Unreleased entry


Resolution: 2.921→40.363 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2634 517 4.85 %
Rwork0.2506 10135 -
obs0.2512 10652 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.71 Å2 / Biso mean: 108.8807 Å2 / Biso min: 9.16 Å2
Refinement stepCycle: final / Resolution: 2.921→40.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 0 0 1714
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011746
X-RAY DIFFRACTIONf_angle_d1.1722364
X-RAY DIFFRACTIONf_chiral_restr0.041281
X-RAY DIFFRACTIONf_plane_restr0.006306
X-RAY DIFFRACTIONf_dihedral_angle_d16.074673
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9211-3.2150.361360.36582460259698
3.215-3.67990.33741140.29862505261998
3.6799-4.63520.28021290.25572542267199
4.6352-40.36710.22211380.2192628276698
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)
11.9171-0.4511-2.49340.40771.85475.06870.1338-0.41170.4602-0.12790.2857-0.0833-0.2797-0.0995-0.33320.92240.1749-0.06810.83450.04490.7002-9.9066-42.34687.223
26.24820.35110.42976.4690.64499.0715-0.15590.2782-0.3729-0.35190.3666-0.98280.35883.2507-0.14170.94050.1557-0.01111.9308-0.19970.7688-21.3829-30.454539.0052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 67 )A2 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 222 )A68 - 222

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