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- PDB-1z5y: Crystal Structure Of The Disulfide-Linked Complex Between The N-T... -

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Basic information

Entry
Database: PDB / ID: 1z5y
TitleCrystal Structure Of The Disulfide-Linked Complex Between The N-Terminal Domain Of The Electron Transfer Catalyst DsbD and The Cytochrome c Biogenesis Protein CcmG
Components
  • Thiol:disulfide interchange protein dsbD
  • Thiol:disulfide interchange protein dsbE
KeywordsOXIDOREDUCTASE/BIOSYNTHETIC PROTEIN / DSBD / N-TERMINAL DOMAIN / IMMUNOGLOBULIN-LIKE / CCMG / THIOREDOXIN-LIKE / DISULFIDE-LINKED / OXIDOREDUCTASE-BIOSYNTHETIC PROTEIN COMPLEX
Function / homology
Function and homology information


protein-disulfide reductase / protein-disulfide reductase (NAD(P)H) activity / cytochrome complex assembly / disulfide oxidoreductase activity / response to copper ion / protein-disulfide reductase activity / cell redox homeostasis / outer membrane-bounded periplasmic space / electron transfer activity / plasma membrane
Similarity search - Function
Periplasmic protein thiol:disulphide oxidoreductase DsbE / 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 ...Periplasmic protein thiol:disulphide oxidoreductase DsbE / 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 / Redoxin / Redoxin / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbE / Thiol:disulfide interchange protein DsbD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsStirnimann, C.U. / Rozhkova, A. / Grauschopf, U. / Gruetter, M.G. / Glockshuber, R. / Capitani, G.
CitationJournal: STRUCTURE / Year: 2005
Title: Structural Basis and Kinetics of DsbD-Dependent Cytochrome c Maturation
Authors: Stirnimann, C.U. / Rozhkova, A. / Grauschopf, U. / Gruetter, M.G. / Glockshuber, R. / Capitani, G.
History
DepositionMar 21, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Thiol:disulfide interchange protein dsbD
E: Thiol:disulfide interchange protein dsbE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4229
Polymers33,0672
Non-polymers3557
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.574, 53.165, 63.833
Angle α, β, γ (deg.)90.00, 104.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15982.631 Da / Num. of mol.: 1 / Fragment: N-Terminal Domain, Residues 1-143 / Mutation: C103S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DSBD, DIPZ, CYCZ, CUTA2, B4136 / Plasmid: PDSBA3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21ROSETTA / References: UniProt: P36655, protein-disulfide reductase
#2: Protein Thiol:disulfide interchange protein dsbE / Cytochrome c biogenesis protein ccmG


Mass: 17084.273 Da / Num. of mol.: 1 / Fragment: Soluble Domain, Residues 43-185 / Mutation: C83S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DSBE, CCMG / Plasmid: pEC86 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21TUNER(DE3) / References: UniProt: P0AA86
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: SODIUM ACETATE, MAGNESIUM CHLORIDE, PEG 4000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.90035 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 23, 2004 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90035 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 26430 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 40.1 Å2 / Rsym value: 0.068 / Net I/σ(I): 19
Reflection shellResolution: 1.94→2.01 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.332 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERv1.2phasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JZD for nDsbD, homology model based on 1KNG for CcmG

1jzd

1kng


Resolution: 1.94→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.27 1902 RANDOM
Rwork0.235 --
obs-25833 -
Displacement parametersBiso mean: 43.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.17 Å20 Å24.27 Å2
2---6.68 Å20 Å2
3---11.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.94→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 23 254 2426
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 1.94→2.01 Å / Rfactor Rfree error: 0.042
RfactorNum. reflection
Rfree0.332 62
Rwork0.306 -
obs-2507

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