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- PDB-1l6p: N-terminal of DsbD (residues 20-144) from E. coli. -

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Basic information

Entry
Database: PDB / ID: 1l6p
TitleN-terminal of DsbD (residues 20-144) from E. coli.
ComponentsThiol:disulfide interchange protein dsbD
KeywordsELECTRON TRANSPORT / disulfide bond isomerase protein / immunoglobulin-like fold
Function / homology
Function and homology information


protein-disulfide reductase / protein-disulfide reductase (NAD(P)H) activity / cytochrome complex assembly / response to copper ion / protein-disulfide reductase activity / cell redox homeostasis / electron transfer activity / plasma membrane
Similarity search - Function
Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / Thiol:disulphide interchange protein DsbD / DsbD gamma / 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-like domain / Thioredoxin-like fold ...Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / Thiol:disulphide interchange protein DsbD / DsbD gamma / 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-like domain / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.65 Å
AuthorsGoulding, C.W. / Sawaya, M.R. / Parseghian, A.
CitationJournal: Biochemistry / Year: 2002
Title: Thiol-disulfide exchange in an immunoglobulin-like fold: structure of the N-terminal domain of DsbD.
Authors: Goulding, C.W. / Sawaya, M.R. / Parseghian, A. / Lim, V. / Eisenberg, D. / Missiakas, D.
History
DepositionMar 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein dsbD


Theoretical massNumber of molelcules
Total (without water)14,1271
Polymers14,1271
Non-polymers00
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.206, 55.630, 102.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-218-

HOH

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Components

#1: Protein Thiol:disulfide interchange protein dsbD / C-type cytochrome biogenesis protein cycZ / Inner membrane copper tolerance protein


Mass: 14126.689 Da / Num. of mol.: 1 / Fragment: Residues 20-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Cell line (production host): DH5alpha cells / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P36655
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, sodium actetate, ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
pH: 7.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein11
20.5 M11pH7.4NaCl
30.1 MTris-HCl11
40.1 Msodium acetate12pH4.6
50.2 Mammonium sulfate11
625 %PEG400011

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 1, 2001 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→26.84 Å / Num. all: 18425 / Num. obs: 18609 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.074 / Net I/σ(I): 28.2
Reflection shellHighest resolution: 1.65 Å / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 5.11 / % possible all: 96.7
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 155538
Reflection shell
*PLUS
% possible obs: 96.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement
RefinementMethod to determine structure: MIR / Resolution: 1.65→10 Å / Num. parameters: 10826 / Num. restraintsaints: 12742 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 783 5 %RANDOM
Rwork0.1385 ---
all0.1408 17500 --
obs0.1408 17500 93.5 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1202.5
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 0 245 1203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0255
X-RAY DIFFRACTIONs_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.065
X-RAY DIFFRACTIONs_approx_iso_adps0.084
LS refinement shellHighest resolution: 1.65 Å
RfactorNum. reflection% reflection
Rfree0.2255 783 -
Rwork0.1385 --
obs-17500 93 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor obs: 0.139 / Rfactor Rfree: 0.215 / Rfactor Rwork: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.137

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