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- PDB-7rgv: Structure of Caulobacter crescentus Suppressor of copper sensitiv... -

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Basic information

Entry
Database: PDB / ID: 7rgv
TitleStructure of Caulobacter crescentus Suppressor of copper sensitivity protein C
ComponentsThioredoxin domain-containing protein
KeywordsOXIDOREDUCTASE / thioredoxin-like / ScsC / isomerase / periplasmic
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Copper resistance protein ScsC, N-terminal / Copper resistance protein ScsC N-terminal domain / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Copper resistance protein ScsC, N-terminal / Copper resistance protein ScsC N-terminal domain / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin domain-containing protein
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsPetit, G.A. / Martin, J.L. / Gulbis, J.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190101613 Australia
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: The suppressor of copper sensitivity protein C from Caulobacter crescentus is a trimeric disulfide isomerase that binds copper(I) with subpicomolar affinity.
Authors: Petit, G.A. / Hong, Y. / Djoko, K.Y. / Whitten, A.E. / Furlong, E.J. / McCoy, A.J. / Gulbis, J.M. / Totsika, M. / Martin, J.L. / Halili, M.A.
History
DepositionJul 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 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: Thioredoxin domain-containing protein


Theoretical massNumber of molelcules
Total (without water)25,1671
Polymers25,1671
Non-polymers00
Water543
1
A: Thioredoxin domain-containing protein

A: Thioredoxin domain-containing protein

A: Thioredoxin domain-containing protein


Theoretical massNumber of molelcules
Total (without water)75,5003
Polymers75,5003
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area3380 Å2
ΔGint-34 kcal/mol
Surface area35350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.948, 113.948, 48.695
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Thioredoxin domain-containing protein


Mass: 25166.631 Da / Num. of mol.: 1 / Mutation: C2S
Source method: isolated from a genetically manipulated source
Details: Linker and TEV scar not visible in the electron densities hence not modelled
Source: (gene. exp.) Caulobacter vibrioides (strain ATCC 19089 / CB15) (bacteria)
Strain: ATCC 19089 / CB15 / Gene: CC_1879 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q9A747
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.51 Å3/Da / Density % sol: 65 % / Description: thick hexagonal crystalline rod
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: Protein reduced with DTT and purified in 25 mM HEPES pH 7.5, 150 mM NaCl. Protein concentrated to 130 mg/ml. 1ul of protein solution mixed with 1ul of crystallant solution: 39% MPD, 200 mM ...Details: Protein reduced with DTT and purified in 25 mM HEPES pH 7.5, 150 mM NaCl. Protein concentrated to 130 mg/ml. 1ul of protein solution mixed with 1ul of crystallant solution: 39% MPD, 200 mM NaAcetate, 20 mM CaCl2 pH 7.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.63→49.34 Å / Num. obs: 10854 / % possible obs: 98.75 % / Redundancy: 12 % / Biso Wilson estimate: 90.52 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.016 / Rrim(I) all: 0.054 / Net I/σ(I): 22.51
Reflection shellResolution: 2.63→2.74 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.46 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 1045 / CC1/2: 0.961 / CC star: 0.99 / Rpim(I) all: 0.431 / Rrim(I) all: 1.52 / % possible all: 94.76

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4VXW res 50-224 chain A

4vxw


Resolution: 2.63→49.34 Å / SU ML: 0.3672 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 40.1233
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Cycle of automated refinement with Phenix + manual refinemetn with Coot. No real space refinement with Phenix, 2 TLS groups 2-63, 64-223. Secondary structure restraint to keep helices in ...Details: Cycle of automated refinement with Phenix + manual refinemetn with Coot. No real space refinement with Phenix, 2 TLS groups 2-63, 64-223. Secondary structure restraint to keep helices in place. Structure has very few crystal contact+ large solvent channel and is expected to be dynamic hence the very high B-factors
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 1081 10.04 %random selection
Rwork0.2237 9685 --
obs0.2263 10766 98.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 122.3 Å2
Refinement stepCycle: LAST / Resolution: 2.63→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 0 3 1670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231695
X-RAY DIFFRACTIONf_angle_d0.44632296
X-RAY DIFFRACTIONf_chiral_restr0.038268
X-RAY DIFFRACTIONf_plane_restr0.0036307
X-RAY DIFFRACTIONf_dihedral_angle_d12.2412636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.750.41081250.3971158X-RAY DIFFRACTION95.46
2.75-2.90.40181350.33821202X-RAY DIFFRACTION99.04
2.9-3.080.36851350.3591191X-RAY DIFFRACTION98
3.08-3.320.33561310.29121190X-RAY DIFFRACTION98.22
3.32-3.650.28841400.26711222X-RAY DIFFRACTION99.63
3.65-4.180.27271360.23691211X-RAY DIFFRACTION99.63
4.18-5.260.22941430.20731229X-RAY DIFFRACTION100
5.27-49.340.20411360.18111282X-RAY DIFFRACTION99.79
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)
11.028903147780.527579996985-0.954395197410.355851261048-1.078153396893.76341067417-0.04356620937030.0693797800539-0.185915009570.3031826626620.0354836092993-0.02952534536910.117329002643-0.12700331590.1270020054791.3660270706-0.09932556848620.02696602397381.10860138712-0.06016051686411.07140248707-4.2888084030253.8391097822-20.35359095
23.03140701353-0.697213244215-0.1797870535352.49198686240.8815348129348.733179635080.194738315168-0.300045965406-0.03460338256560.339321586411-0.113557340233-0.09831068279070.4721628399870.0360600855654-0.1326023250021.23616635526-0.188964977298-0.07290277610820.77424277110.1363801726221.00934847009-17.974037007141.95638993419.0932395607
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 63 )2 - 631 - 62
22chain 'A' and (resid 64 through 223 )64 - 22363 - 222

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