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- PDB-1g0t: DSBC MUTANT C101S -

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Basic information

Entry
Database: PDB / ID: 1g0t
TitleDSBC MUTANT C101S
ComponentsTHIOL:DISULFIDE INTERCHANGE PROTEIN DSBC
KeywordsISOMERASE / thiol oxidoreductase / protein disulfide bond isomerase / thioredoxin fold
Function / homology
Function and homology information


response to copper ion / protein disulfide isomerase activity / protein-disulfide reductase activity / chaperone-mediated protein folding / outer membrane-bounded periplasmic space / periplasmic space / protein homodimerization activity
Similarity search - Function
Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase, DsbC/G / Disulfide bond isomerase protein N-terminal domain / : / Thioredoxin-like domain / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. ...Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase, DsbC/G / Disulfide bond isomerase protein N-terminal domain / : / Thioredoxin-like domain / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Nuclear Transport Factor 2; Chain: A, / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Thiol:disulfide interchange protein DsbC / Thiol:disulfide interchange protein DsbC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsHaebel, P.W. / Metcalf, P.
Citation
Journal: Embo J. / Year: 2002
Title: Crystal structure of the protein disulfide bond isomerase, DsbC, from Escherichia coli
Authors: Haebel, P.W. / Goldstone, D. / Katzen, F. / Beckwith, J. / Metcalf, P.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: The disulfide bond isomerase DsbC is activated by an immunoglobulin-fold thiol oxidoreductase: crystal structure of the DsbC-DsbDalpha complex
Authors: McCarthy, A.A. / Haebel, P.W. / Torronen, A. / Rybin, V. / Baker, E.N. / Metcalf, P.
History
DepositionOct 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBC
B: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0503
Polymers46,9442
Non-polymers1061
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-12 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.441, 78.501, 95.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein THIOL:DISULFIDE INTERCHANGE PROTEIN DSBC / E.C.5.3.4.1 / PROTEIN DISULFIDE BOND ISOMERASE


Mass: 23471.949 Da / Num. of mol.: 2 / Mutation: C101S
Source method: isolated from a genetically manipulated source
Details: ACTIVE SITE MUTANT C101S / Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: PERIPLASM / Plasmid: PET22B / Production host: Escherichia coli (E. coli)
References: UniProt: P21892, UniProt: P0AEG6*PLUS, protein disulfide-isomerase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.39 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 23-25% PEG 550MME, 100mM Tris/HCl pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 14441 / Num. obs: 14441 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 23.8
Reflection shellResolution: 2.6→2.76 Å / Rmerge(I) obs: 0.442 / Num. unique all: 2189 / % possible all: 94.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.6→29.72 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 287411.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 699 5 %RANDOM
Rwork0.212 ---
obs0.212 13945 97.5 %-
all-13945 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.87 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.95 Å20 Å20 Å2
2--6.21 Å20 Å2
3----2.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 0 60 3331
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 109 5 %
Rwork0.212 2080 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PA
X-RAY DIFFRACTION3WATER_REP.PARA
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5PEG_XPLOR_PAR.TXT

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