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- PDB-2fwf: high resolution crystal structure of the C-terminal domain of the... -

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Basic information

Entry
Database: PDB / ID: 2fwf
Titlehigh resolution crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (reduced form)
ComponentsThiol:disulfide interchange protein dsbD
KeywordsOXIDOREDUCTASE / DSBD / THIOREDOXIN-LIKE / C-terminal domain / reduced form
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:disulphide interchange protein DsbD / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / 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 domain / Thioredoxin-like / Thioredoxin-like domain / Thioredoxin-like fold ...Thiol:disulphide interchange protein DsbD / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / 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 domain / Thioredoxin-like / Thioredoxin-like domain / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Thiol:disulfide interchange protein DsbD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsStirnimann, C.U. / Rozhkova, A. / Grauschopf, U. / Boeckmann, R.A. / Glockshuber, R. / Capitani, G. / Gruetter, M.G.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: High-resolution structures of Escherichia coli cDsbD in different redox states: A combined crystallographic, biochemical and computational study
Authors: Stirnimann, C.U. / Rozhkova, A. / Grauschopf, U. / Boeckmann, R.A. / Glockshuber, R. / Capitani, G. / Gruetter, M.G.
History
DepositionFeb 2, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein dsbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,03210
Polymers15,0981
Non-polymers9349
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.355, 46.082, 74.143
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 dsbD / Protein-disulfide reductase / Disulfide reductase / C-type cytochrome biogenesis protein cycZ / ...Protein-disulfide reductase / Disulfide reductase / C-type cytochrome biogenesis protein cycZ / Inner membrane copper tolerance protein


Mass: 15097.932 Da / Num. of mol.: 1 / Fragment: C-Terminal Domain, Residues 419-546
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): BL21 ROSETTA / References: UniProt: P36655, protein-disulfide reductase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.61 Å3/Da / Density % sol: 28.35 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M ammonium acetate, 0.2M sodium acetate, 0.1M sodium iodide, 40% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 25, 2003 / Details: dynamically bendable mirror
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. obs: 25864 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 12.4 Å2 / Rsym value: 0.091 / Net I/σ(I): 20.8
Reflection shellResolution: 1.3→1.35 Å / Mean I/σ(I) obs: 3.1 / Num. unique all: 2253 / Rsym value: 0.288 / % possible all: 87

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: modified version of 2TRX (see publication)

2trx


Resolution: 1.3→15 Å / Num. parameters: 4882 / Num. restraintsaints: 4354 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.198 778 RANDOM
Rwork0.17 --
all-25054 -
obs-25027 -
Refine analyzeNum. disordered residues: 23 / Occupancy sum hydrogen: 0.5 / Occupancy sum non hydrogen: 1122.07
Refinement stepCycle: LAST / Resolution: 1.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 13 172 1200
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0271
X-RAY DIFFRACTIONs_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0.057
LS refinement shellHighest resolution: 1.3 Å
RfactorNum. reflection
Rfree0.18 627
Rwork0.16 -
obs-20614

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