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- PDB-1eej: CRYSTAL STRUCTURE OF THE PROTEIN DISULFIDE BOND ISOMERASE, DSBC, ... -

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Basic information

Entry
Database: PDB / ID: 1eej
TitleCRYSTAL STRUCTURE OF THE PROTEIN DISULFIDE BOND ISOMERASE, DSBC, FROM ESCHERICHIA COLI
ComponentsTHIOL:DISULFIDE INTERCHANGE PROTEIN
KeywordsISOMERASE / OXIDOREDUCTASE / PROTEIN DISULFIDE ISOMERASE / PROTEIN FOLDING / REDOX PROTEIN / REDOX-ACTIVE CENTER
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 / Disulfide bond isomerase protein N-terminal domain / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G / Thioredoxin-like domain / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. ...Disulphide bond isomerase, DsbC/G, N-terminal / Disulfide bond isomerase protein N-terminal domain / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G / 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
Thiol:disulfide interchange protein DsbC / Thiol:disulfide interchange protein DsbC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMcCarthy, A.A. / Haebel, P.W. / Torronen, A. / Rybin, V. / Baker, E.N. / Metcalf, P.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of the protein disulfide bond isomerase, DsbC, from Escherichia coli.
Authors: McCarthy, A.A. / Haebel, P.W. / Torronen, A. / Rybin, V. / Baker, E.N. / Metcalf, P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: CRYSTALLIZATION OF DSBC, THE DISULFIDE BOND ISOMERASE FROM ESCHERICHIA COLI
Authors: RYBIN, V. / ZAPUN, A. / TORRONEN, A. / RAINA, S. / MISSIAKAS, D. / CREIGHTON, T. / METCALF, P.
History
DepositionJan 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,1713
Polymers46,9762
Non-polymers1951
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-15 kcal/mol
Surface area21350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.336, 78.149, 94.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer

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Components

#1: Protein THIOL:DISULFIDE INTERCHANGE PROTEIN / PROTEIN DISULFIDE-ISOMERASE / DSBC


Mass: 23488.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: PERIPLASM / Production host: Bacteria (eubacteria)
References: UniProt: P21892, UniProt: P0AEG6*PLUS, protein disulfide-isomerase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 550 (MME), MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
225 %PEG40001reservoir
350 %isopropanol1reservoir

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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: Oct 29, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 561577 / Num. obs: 35436 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.322 / Num. unique all: 3468 / % possible all: 99.5
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS0.9refinement
RefinementResolution: 1.9→29.21 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 865666.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3394 10 %RANDOM
Rwork0.214 ---
all0.214 35330 --
obs0.214 34017 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 79.08 Å2 / ksol: 0.43 e/Å3
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.91 Å20 Å20 Å2
2--6.84 Å20 Å2
3---0.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 12 217 3509
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.021.5
X-RAY DIFFRACTIONc_mcangle_it2.92
X-RAY DIFFRACTIONc_scbond_it32
X-RAY DIFFRACTIONc_scangle_it4.322.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 515 9.7 %
Rwork0.245 4806 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4CIS_PEPTIDE.P
X-RAY DIFFRACTION5MES.PAR
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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