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- PDB-6dxn: 1.95 Angstrom Resolution Crystal Structure of DsbA Disulfide Inte... -

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Basic information

Entry
Database: PDB / ID: 6dxn
Title1.95 Angstrom Resolution Crystal Structure of DsbA Disulfide Interchange Protein from Klebsiella pneumoniae.
ComponentsThiol:disulfide interchange protein
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / DsbA oxidoreductase / Oxidoreductases.
Function / homology
Function and homology information


periplasmic space / oxidoreductase activity
Similarity search - Function
Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMinasov, G. / Wawrzak, Z. / Shuvalova, L. / Kiryukhina, O. / Endres, M. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionJun 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
C: Thiol:disulfide interchange protein
D: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9957
Polymers87,5454
Non-polymers4513
Water6,575365
1
A: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0362
Polymers21,8861
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0362
Polymers21,8861
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0362
Polymers21,8861
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thiol:disulfide interchange protein


Theoretical massNumber of molelcules
Total (without water)21,8861
Polymers21,8861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.401, 42.392, 103.949
Angle α, β, γ (deg.)90.27, 89.78, 96.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Thiol:disulfide interchange protein


Mass: 21886.145 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: BB785_17655, BKY56_010280, C3F39_04655 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: A0A169B8J1
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 9.6mg/ml, 0.01M Tris-HCl pH 8.3; Screen: PEGs II (B9), 0.1M Tris-HCl pH 8.5, 30% (v/v) PEG 400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 11, 2018 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.43
11K, H, -L20.15
11-K, -H, -L30.128
11-h,-k,l40.292
ReflectionResolution: 1.95→30 Å / Num. obs: 51946 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.073 / Rrim(I) all: 0.154 / Rsym value: 0.135 / Χ2: 1.759 / Net I/σ(I): 16.8
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2517 / CC1/2: 0.726 / Rpim(I) all: 0.43 / Rrim(I) all: 0.897 / Rsym value: 0.786 / Χ2: 1.076 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-3000data reduction
HKL-3000data scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OCF

4ocf


Resolution: 1.95→27.01 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.911 / SU B: 2.991 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22982 2397 4.7 %RANDOM
Rwork0.17973 ---
obs0.18213 48932 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.852 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å212.88 Å20.65 Å2
2--3.66 Å2-13.9 Å2
3----3.3 Å2
Refinement stepCycle: 1 / Resolution: 1.95→27.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6032 0 30 365 6427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0146323
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175815
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.6838556
X-RAY DIFFRACTIONr_angle_other_deg0.4271.70613621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7125785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.58624.175309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.702151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8811520
X-RAY DIFFRACTIONr_chiral_restr0.0560.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0380.027078
X-RAY DIFFRACTIONr_gen_planes_other0.0340.021186
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6712.2593110
X-RAY DIFFRACTIONr_mcbond_other1.672.2593109
X-RAY DIFFRACTIONr_mcangle_it2.5993.3823905
X-RAY DIFFRACTIONr_mcangle_other2.5983.3823906
X-RAY DIFFRACTIONr_scbond_it1.6252.3883213
X-RAY DIFFRACTIONr_scbond_other1.6242.3883213
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3873.5194652
X-RAY DIFFRACTIONr_long_range_B_refined4.32926.8037313
X-RAY DIFFRACTIONr_long_range_B_other4.23226.7837264
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 176 -
Rwork0.177 2835 -
obs--78.23 %

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