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- PDB-4npb: The crystal structure of thiol:disulfide interchange protein DsbC... -

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Basic information

Entry
Database: PDB / ID: 4npb
TitleThe crystal structure of thiol:disulfide interchange protein DsbC from Yersinia pestis CO92
ComponentsProtein disulfide isomerase II
KeywordsISOMERASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


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. / Nuclear Transport Factor 2; Chain: A, / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / PHOSPHATE ION / Thiol:disulfide interchange protein / Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.147 Å
AuthorsTan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of thiol:disulfide interchange protein DsbC from Yersinia pestis CO92
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionNov 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein disulfide isomerase II
B: Protein disulfide isomerase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5645
Polymers49,0312
Non-polymers5323
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-20 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.894, 141.335, 41.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsExperimentally unknown. It is predicted that the chains A and B form a dimer.

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Components

#1: Protein Protein disulfide isomerase II / Thiol:disulfide interchange protein (DsbC)


Mass: 24515.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: dsbC, y3275, Yersinia pestis, YPO0891, YP_3587 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q7CGT8, UniProt: A0A5P8YD62*PLUS
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.056M Sodium Phosphate monobasic monohydrate, 1.344M potassium phosphate dibasic, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.15→30.1 Å / Num. all: 29556 / Num. obs: 29556 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 5.8 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 28.8
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.57 / % possible all: 97.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.147→30.505 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 1497 5.07 %
Rwork0.1918 --
obs0.194 29507 98.87 %
all-29508 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.147→30.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 33 62 3366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083363
X-RAY DIFFRACTIONf_angle_d1.0684563
X-RAY DIFFRACTIONf_dihedral_angle_d14.5631251
X-RAY DIFFRACTIONf_chiral_restr0.067528
X-RAY DIFFRACTIONf_plane_restr0.004588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.147-2.21630.34081290.27892442X-RAY DIFFRACTION96
2.2163-2.29540.3131430.25482471X-RAY DIFFRACTION98
2.2954-2.38730.33351390.24812476X-RAY DIFFRACTION99
2.3873-2.49590.28881440.22422514X-RAY DIFFRACTION99
2.4959-2.62740.28971280.23122534X-RAY DIFFRACTION99
2.6274-2.79190.28991250.22972539X-RAY DIFFRACTION99
2.7919-3.00730.3071410.23732537X-RAY DIFFRACTION99
3.0073-3.30970.2611350.22532542X-RAY DIFFRACTION99
3.3097-3.78780.24391370.18312597X-RAY DIFFRACTION100
3.7878-4.76930.16691420.14422602X-RAY DIFFRACTION100
4.7693-30.5080.1771340.15972756X-RAY DIFFRACTION99
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)
12.2171-0.6698-1.59653.582.54759.0660.0193-0.1309-0.0321-0.0837-0.07690.0006-0.6509-0.24740.06460.22320.0329-0.02980.33230.0250.40431.282138.285217.7985
23.51843.6955-4.42874.4799-5.80497.7959-0.14810.2708-0.0051-0.5743-0.2320.3604-0.0563-0.19470.38440.3101-0.0066-0.07810.3351-0.02660.30326.632846.95294.0603
32.331-0.2668-0.13385.19981.80242.8924-0.00740.03430.1039-0.28670.0553-0.2807-0.28810.0625-0.03910.35520.0109-0.00040.28450.02550.201319.898253.2361.1443
43.95860.14611.51036.08763.56069.3114-0.0026-0.0045-0.33860.2122-0.20310.33140.8882-0.450.17970.3117-0.01390.03440.35670.03730.5184.851522.523317.684
52.5557-0.8599-0.19535.52760.51543.43250.0691-0.09430.05230.22760.0985-0.37880.1847-0.1031-0.16570.3182-0.0204-0.06650.2750.02170.246227.325518.896932.8937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 235 )
4X-RAY DIFFRACTION4chain 'B' and (resid 21 through 82 )
5X-RAY DIFFRACTION5chain 'B' and (resid 83 through 235 )

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