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- PDB-6c29: Crystal structure of the N-terminal periplasmic domain of ScsB fr... -

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Basic information

Entry
Database: PDB / ID: 6c29
TitleCrystal structure of the N-terminal periplasmic domain of ScsB from Proteus mirabilis
ComponentsPutative metal resistance protein
KeywordsOXIDOREDUCTASE / redox enzyme / immunoglobulin fold / cysteine active site
Function / homology
Function and homology information


cytochrome complex assembly / membrane
Similarity search - Function
DsbD gamma / Thioredoxin-like / Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal / Cytochrome C biogenesis protein, transmembrane domain / Cytochrome C biogenesis protein transmembrane region / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin-like superfamily
Similarity search - Domain/homology
Metal resistance protein
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.538 Å
AuthorsFurlong, E.J. / Choudhury, H.G. / Kurth, F. / Martin, J.L.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)FL0992138, J.L.M. Australia
Australian Research Council (ARC)DP130100576 Australia
CitationJournal: J Biol Chem / Year: 2018
Title: Disulfide isomerase activity of the dynamic, trimeric ScsC protein is primed by the tandem immunoglobulin-fold domain of ScsB.
Authors: Emily J Furlong / Hassanul G Choudhury / Fabian Kurth / Anthony P Duff / Andrew E Whitten / Jennifer L Martin /
Abstract: Correct disulfide bond formation is essential for proper folding of many proteins, including bacterial virulence factors. The suppressor of copper sensitivity (Scs) proteins have roles in ...Correct disulfide bond formation is essential for proper folding of many proteins, including bacterial virulence factors. The suppressor of copper sensitivity (Scs) proteins have roles in dithiol/disulfide interchange and the bacterial response to copper stress. Encoded in a four-gene cassette (ScsABCD) present in many Gram-negative bacteria, the Scs proteins are enigmatic and poorly characterized. Here, we show that the periplasmic α-domain of the membrane protein ScsB in the Gram-negative bacterium forms a redox relay with the soluble periplasmic protein PmScsC. We also found that the periplasmic α-domain is sufficient to activate the disulfide isomerase activity of PmScsC. The crystal structure of PmScsBα at a resolution of 1.54 Å revealed that it comprises two structurally similar immunoglobulin-like folds, one of which includes a putative redox-active site with the sequence CC. We confirmed the importance of these cysteine residues for PmScsBα function, and in addition, we engineered cysteine variants that produced a stable complex between PmScsC and PmScsBα. Using small-angle X-ray and neutron scattering analyses with contrast variation, we determined a low-resolution structure of the PmScsC-PmScsBα complex. The structural model of this complex suggested that PmScsBα uses both of its immunoglobulin-like folds to interact with PmScsC and revealed that the highly dynamic PmScsC becomes ordered upon PmScsBα binding. These findings add to our understanding of the poorly characterized Scs proteins.
History
DepositionJan 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative metal resistance protein
B: Putative metal resistance protein
C: Putative metal resistance protein


Theoretical massNumber of molelcules
Total (without water)84,2493
Polymers84,2493
Non-polymers00
Water12,052669
1
A: Putative metal resistance protein


Theoretical massNumber of molelcules
Total (without water)28,0831
Polymers28,0831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative metal resistance protein


Theoretical massNumber of molelcules
Total (without water)28,0831
Polymers28,0831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative metal resistance protein


Theoretical massNumber of molelcules
Total (without water)28,0831
Polymers28,0831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.977, 97.061, 110.196
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 1 - 247 / Label seq-ID: 1 - 247

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC

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Components

#1: Protein Putative metal resistance protein


Mass: 28083.121 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (strain HI4320) (bacteria)
Strain: HI4320 / Gene: PMI0439 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: B4EV20
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES monohydrate pH 6, 6% v/v tacsimate pH 6, 24% PEG4000, 4% 1,3-butanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.538→97.061 Å / Num. obs: 111511 / % possible obs: 99.7 % / Redundancy: 15.8 % / Biso Wilson estimate: 15.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.038 / Rrim(I) all: 0.15 / Net I/σ(I): 16
Reflection shellResolution: 1.538→1.544 Å / Redundancy: 16.3 % / Rmerge(I) obs: 2.114 / Num. unique obs: 1094 / CC1/2: 0.653 / Rpim(I) all: 0.531 / Rrim(I) all: 2.18 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Blu-Icedata collection
XDSdata reduction
Aimless0.5.8data scaling
PHASER2.5.7phasing
BUCCANEER1.5model building
Coot0.8.1model building
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.538→55.098 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.95
Details: The structure was solved initially by using SAD with SHELX in hkl2map to get a partial alanine model of the protein. This model was then used for MR in Phaser
RfactorNum. reflection% reflection
Rfree0.1978 5541 4.97 %
Rwork0.1726 --
obs0.1738 111388 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.77 Å2 / Biso mean: 27.6084 Å2 / Biso min: 8.36 Å2
Refinement stepCycle: final / Resolution: 1.538→55.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5694 0 0 669 6363
Biso mean---31.78 -
Num. residues----741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116045
X-RAY DIFFRACTIONf_angle_d1.3328351
X-RAY DIFFRACTIONf_chiral_restr0.058944
X-RAY DIFFRACTIONf_plane_restr0.0071098
X-RAY DIFFRACTIONf_dihedral_angle_d12.1912183
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3908X-RAY DIFFRACTION11.212TORSIONAL
12B3908X-RAY DIFFRACTION11.212TORSIONAL
13C3908X-RAY DIFFRACTION11.212TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5384-1.55590.29262150.2493470368599
1.5559-1.57420.25091900.23643458364899
1.5742-1.59340.27421770.22693489366699
1.5934-1.61360.25941860.219634743660100
1.6136-1.63480.24541810.22123470365199
1.6348-1.65720.22631600.20573491365199
1.6572-1.68090.21581850.20083502368799
1.6809-1.7060.21441820.19383503368599
1.706-1.73260.26741550.202135143669100
1.7326-1.7610.23821720.193234963668100
1.761-1.79140.20781820.18635243706100
1.7914-1.8240.19491760.189534753651100
1.824-1.85910.24321780.182835183696100
1.8591-1.8970.19911960.190535433739100
1.897-1.93830.25511770.23043459363699
1.9383-1.98330.21371710.174135413712100
1.9833-2.03290.20391890.165635053694100
2.0329-2.08790.18931840.17735193703100
2.0879-2.14940.21011880.168235283716100
2.1494-2.21870.21712070.167235153722100
2.2187-2.2980.21422030.188535203723100
2.298-2.390.18291830.16435413724100
2.39-2.49880.2171770.170735553732100
2.4988-2.63060.19881720.171335663738100
2.6306-2.79540.2021890.176835783767100
2.7954-3.01120.18742050.1735433748100
3.0112-3.31420.18081740.163935953769100
3.3142-3.79360.1772060.151635933799100
3.7936-4.77920.16711860.135936463832100
4.7792-55.13330.16421950.16633716391198
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)
10.7257-0.10680.24120.2458-0.09570.48570.0383-0.12360.04450.1989-0.06790.0085-0.01540.0513-0.0050.14580.0211-0.03210.13050.02850.111818.905827.5779-21.1611
20.4790.30020.32070.19730.19260.8862-0.02610.0624-0.0006-0.0590.01510.02690.03570.1393-0.02040.10040.0309-0.01170.12560.01350.114318.952228.9265-33.052
30.50540.4983-0.10930.98350.10510.5406-0.35290.30660.1166-0.83740.43560.41620.27040.44460.0655-0.02220.19780.22540.25-0.1223-0.15523.351522.0495-36.5323
40.5090.2097-0.13070.1271-0.01560.4876-0.0055-0.06180.1424-0.07130.05670.0989-0.09030.0520.00590.11420.0265-0.01230.10820.00490.118213.185633.1562-36.8198
50.62190.123-0.01670.1280.1690.42950.0282-0.0119-0.07760.0449-0.04710.09240.03350.1922-0.01740.120.0357-0.02440.1530.02330.164924.94528.6272-27.6349
60.66950.063-0.00370.41670.06140.0704-0.023-0.1907-0.21680.0184-0.0049-0.0187-0.0089-0.07-0.05180.10850.03350.01890.15070.0580.146611.81816.8426-32.1219
70.2437-0.18950.0940.1030.00440.16050.08120.03930.0228-0.4221-0.11370.02920.04750.19030.00020.23960.04810.02950.178-0.00330.164310.763532.3161-61.3192
80.4057-0.4727-0.03670.6455-0.31640.64710.052-0.00690.0223-0.1562-0.0713-0.0144-0.00060.08360.00270.11420.0162-0.00380.1151-0.01090.11527.457733.9056-53.9059
9-0.0103-0.04560.05910.2106-0.34950.62280.08730.20010.5554-0.3053-0.4169-0.42090.18430.5434-0.06560.1087-0.09440.05390.25440.06520.475624.192841.4761-56.9161
100.2252-0.26420.11370.2505-0.01050.19410.0860.07540.0151-0.1383-0.007-0.0020.02550.08030.04720.1020.03890.01650.13080.00350.100711.138226.2494-52.7609
110.88320.0535-0.28720.602-0.04010.47740.00960.0820.0963-0.0466-0.0543-0.0668-0.07880.0817-0.01340.1148-0.0089-0.01540.10080.02810.1164-3.709127.1919-28.5442
120.49350.58220.1060.46810.15480.68490.126-0.0965-0.05660.2489-0.10730.0508-0.0427-0.09140.01450.1547-0.02370.00090.12610.00810.1248-12.943221.6454-20.8047
130.8440.5489-0.28680.8023-0.41570.2587-0.11490.12220.0427-0.04290.0748-0.0055-0.15820.0086-0.13030.1591-0.0072-0.0170.11160.01190.088-10.184828.0673-29.6377
140.8256-0.16430.23331.5694-0.41120.41410.0562-0.13580.00130.1473-0.01250.161-0.0504-0.11990.02920.11190.00290.01650.146-0.03130.1304-26.97938.0757-18.5285
150.69110.3884-0.04571.6710.01130.55460.01410.01950.0211-0.07410.066-0.0759-0.03020.02810.12870.1015-0.01070.02510.1025-0.01070.1133-17.480654.394-2.8791
160.42550.16620.41020.53030.4690.5648-0.0344-0.0149-0.0516-0.09890.06390.0963-0.07450.00660.01190.1421-0.0224-0.00570.1051-0.01270.1259-24.232547.3823-3.6126
170.43930.59630.02590.9368-0.37950.617-0.00890.0376-0.0493-0.0947-0.0114-0.1721-0.02820.13670.00050.1082-0.00670.0320.147-0.00780.1368-14.282850.5504-5.286
181.26780.2443-0.41370.9173-0.12360.6292-0.07550.1054-0.0096-0.11590.08860.12840.0523-0.0591-0.01450.1599-0.0147-0.02910.12090.00870.0954-35.174831.8513-2.3665
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 60 )A25 - 60
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 74 )A61 - 74
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 97 )A75 - 97
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 128 )A98 - 128
6X-RAY DIFFRACTION6chain 'A' and (resid 129 through 154 )A129 - 154
7X-RAY DIFFRACTION7chain 'A' and (resid 155 through 173 )A155 - 173
8X-RAY DIFFRACTION8chain 'A' and (resid 174 through 210 )A174 - 210
9X-RAY DIFFRACTION9chain 'A' and (resid 211 through 225 )A211 - 225
10X-RAY DIFFRACTION10chain 'A' and (resid 226 through 247 )A226 - 247
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 45 )B1 - 45
12X-RAY DIFFRACTION12chain 'B' and (resid 46 through 89 )B46 - 89
13X-RAY DIFFRACTION13chain 'B' and (resid 90 through 154 )B90 - 154
14X-RAY DIFFRACTION14chain 'B' and (resid 155 through 247 )B155 - 247
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 60 )C1 - 60
16X-RAY DIFFRACTION16chain 'C' and (resid 61 through 89 )C61 - 89
17X-RAY DIFFRACTION17chain 'C' and (resid 90 through 154 )C90 - 154
18X-RAY DIFFRACTION18chain 'C' and (resid 155 through 247 )C155 - 247

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