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- PDB-6mhh: Proteus mirabilis ScsC linker (residues 39-49) deletion and N6K mutant -

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Basic information

Entry
Database: PDB / ID: 6mhh
TitleProteus mirabilis ScsC linker (residues 39-49) deletion and N6K mutant
ComponentsMetal resistance protein
KeywordsISOMERASE / Disulfide bond / 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
Putative metal resistance protein
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.083 Å
AuthorsFurlong, E.J. / 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
DepositionSep 17, 2018Deposition site: RCSB / Processing site: RCSB
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.journal_volume / _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

Downloads & links

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Assembly

Deposited unit
A: Metal resistance protein


Theoretical massNumber of molelcules
Total (without water)23,4831
Polymers23,4831
Non-polymers00
Water2,360131
1
A: Metal resistance protein

A: Metal resistance protein

A: Metal resistance protein


Theoretical massNumber of molelcules
Total (without water)70,4493
Polymers70,4493
Non-polymers00
Water543
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 area8200 Å2
ΔGint-46 kcal/mol
Surface area28160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.040, 64.040, 299.834
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-393-

HOH

21A-403-

HOH

31A-431-

HOH

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Components

#1: Protein Metal resistance protein


Mass: 23483.092 Da / Num. of mol.: 1 / Mutation: 11-residue linker region (39-49) deleted; N6K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Strain: HI4320 / Gene: PMI0440 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4EV21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 51.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7, 32% v/v Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.08→24.99 Å / Num. obs: 14715 / % possible obs: 99.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 21.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.02 / Rrim(I) all: 0.063 / Net I/σ(I): 27.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.08-2.147.80.1411350.9970.0530.15100
9.08-24.998.80.0612070.9960.0220.06594.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.8data scaling
PDB_EXTRACT3.24data extraction
iMOSFLM7.1.3data reduction
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XVW (chain A, residues 47-224)

4xvw


Resolution: 2.083→24.986 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.05
RfactorNum. reflection% reflection
Rfree0.2096 727 4.94 %
Rwork0.1742 --
obs0.1759 14704 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.01 Å2 / Biso mean: 34.3325 Å2 / Biso min: 9.34 Å2
Refinement stepCycle: final / Resolution: 2.083→24.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 0 131 1758
Biso mean---33.35 -
Num. residues----211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031705
X-RAY DIFFRACTIONf_angle_d0.6872325
X-RAY DIFFRACTIONf_chiral_restr0.029281
X-RAY DIFFRACTIONf_plane_restr0.003300
X-RAY DIFFRACTIONf_dihedral_angle_d11.469670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.083-2.24380.25681360.181227192855
2.2438-2.46940.19131540.171327522906
2.4694-2.82630.19251370.174527802917
2.8263-3.55920.21911620.181827902952
3.5592-24.9880.20491380.168529363074
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)
10.049-0.0670.00320.0682-0.01110.0449-0.1378-0.01820.10660.0554-0.04510.06920.21050.1141-0.10390.18030.0104-0.02980.1965-0.00130.10961.2429-41.226557.5973
20.0248-0.00080.03570.0113-0.00560.03560.1409-0.0256-0.05260.10680.09150.1587-0.1394-0.0526-0.00010.31470.0065-0.02440.26660.01810.1743-4.5565-28.448939.5314
30.2013-0.03910.10010.0534-0.03780.07280.0379-0.0376-0.09340.03210.0093-0.0067-0.162-0.05780.06130.19170.0071-0.00310.0799-0.01610.1414-5.3746-15.750622.0412
40.0157-0.02540.05890.0397-0.08420.1979-0.0291-0.04960.0655-0.06170.17520.12920.0731-0.33350.01120.1336-0.00050.01040.14560.03560.2905-15.6302-22.693615.8688
50.0921-0.05870.02350.0804-0.03450.1738-0.0310.038-0.22020.0863-0.01540.1267-0.0404-0.15050.02030.15760.0278-0.00450.0836-0.01010.2156-7.5124-19.597919.523
60.08980.08860.05680.1641-0.00490.2449-0.08230.1299-0.0549-0.16850.13060.1273-0.09640.1470.0590.1482-0.0237-0.03270.1187-0.00060.1573-2.6435-17.97928.6488
70.08610.12670.04860.5093-0.08120.10720.05480.197-0.1808-0.11190.10860.18690.34640.25930.03630.24940.103-0.09420.2014-0.0450.1787-3.3215-25.36551.1152
80.2766-0.04340.24350.580.14250.30560.10630.0215-0.04850.21320.02860.1027-0.01220.08650.05990.12520.0021-0.0130.13670.03070.1677-0.827-22.097819.471
90.00010.0004-0.0028-0.00230.00370.0028-0.005-0.1676-0.1120.0812-0.00120.11740.0061-0.05020.09010.2059-0.06520.37590.5303-0.00380.4418-20.7049-18.778428.7066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 53 )A25 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 84 )A54 - 84
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 100 )A85 - 100
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 115 )A101 - 115
6X-RAY DIFFRACTION6chain 'A' and (resid 116 through 145 )A116 - 145
7X-RAY DIFFRACTION7chain 'A' and (resid 146 through 162 )A146 - 162
8X-RAY DIFFRACTION8chain 'A' and (resid 163 through 207 )A163 - 207
9X-RAY DIFFRACTION9chain 'A' and (resid 208 through 222 )A208 - 222

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