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- PDB-2rem: Crystal Structure of oxidoreductase DsbA from Xylella fastidiosa -

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Basic information

Entry
Database: PDB / ID: 2rem
TitleCrystal Structure of oxidoreductase DsbA from Xylella fastidiosa
Components
  • 8 residue peptide
  • Disulfide oxidoreductase
KeywordsOXIDOREDUCTASE / disulfide oxidoreductase / DSBA / thioredoxin fold / redox-active center
Function / homology
Function and homology information


cell redox homeostasis / periplasmic space
Similarity search - Function
Thioredoxin / Thioredoxin-like fold / Thiol:disulphide interchange protein DsbA/DsbL / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Thioredoxin / Thioredoxin-like fold / Thiol:disulphide interchange protein DsbA/DsbL / 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
Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsRinaldi, F.C. / Guimaraes, B.G.
CitationJournal: To be Published
Title: Residues substitution in the active site of DSBA may compensate for the lack of the canonical motif CPHC
Authors: Rinaldi, F.C. / Guimaraes, B.G.
History
DepositionSep 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disulfide oxidoreductase
B: Disulfide oxidoreductase
C: Disulfide oxidoreductase
T: 8 residue peptide


Theoretical massNumber of molelcules
Total (without water)64,6994
Polymers64,6994
Non-polymers00
Water8,737485
1
A: Disulfide oxidoreductase


Theoretical massNumber of molelcules
Total (without water)21,3331
Polymers21,3331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Disulfide oxidoreductase


Theoretical massNumber of molelcules
Total (without water)21,3331
Polymers21,3331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Disulfide oxidoreductase
T: 8 residue peptide


Theoretical massNumber of molelcules
Total (without water)22,0322
Polymers22,0322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)200.117, 41.722, 79.807
Angle α, β, γ (deg.)90.000, 95.870, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Disulfide oxidoreductase


Mass: 21333.254 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (bacteria) / Gene: XF1436 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3)
References: UniProt: Q9PDE3, protein-disulfide reductase (glutathione)
#2: Protein/peptide 8 residue peptide


Mass: 698.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (bacteria)
Description: CHAIN T IS DERIVED FROM THE EXPRESSION SYSTEM THAT WAS CO-PURIFIED WITH THE PROTEIN (XFDSBA)
Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ACTUAL SEQUENCE OF CHAIN T IS UNKNOWN. THESE RESIDUES WERE MODELED AS UNK DUE TO WEAK ELECTRON DENSITY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 30% PEG 4000, 0.1M acetate chloride, Guanidine Hydrochloride, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONLNLS D03B-MX111.431
SYNCHROTRONNSLS X26C20.9795
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJan 26, 2005
ADSC QUANTUM 42CCDApr 24, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single Crystal Monochromator Si(111)SINGLE WAVELENGTHMx-ray1
2Single Crystal Monochromator Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.4311
20.97951
ReflectionRedundancy: 6.6 % / Av σ(I) over netI: 22.6 / Number: 360459 / Rmerge(I) obs: 0.079 / Χ2: 4.32 / D res high: 1.85 Å / D res low: 50 Å / Num. obs: 54206 / % possible obs: 91.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.995098.610.0628.6376.4
3.163.9981.510.0535.3636.6
2.763.1699.910.0654.8937.2
2.512.7610010.0854.0087.3
2.332.5110010.1073.4657.3
2.192.3351.410.1593.7975
2.082.1910010.1952.8817.1
1.992.0899.910.2282.5187.3
1.921.9999.510.4663.4256.3
1.851.9283.610.3134.6364.9
ReflectionResolution: 1.9→50 Å / Num. all: 52300 / Num. obs: 52143 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.074 / Χ2: 0.754 / Net I/σ(I): 7.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.479 / Num. unique all: 5052 / Χ2: 1.366 / % possible all: 98.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
PDB_EXTRACT3data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.699 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2657 5.1 %RANDOM
Rwork0.183 ---
all0.204 52367 --
obs0.185 52137 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.959 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.36 Å2
2--1.09 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4489 0 0 485 4974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224614
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9396288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4755579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2722.431218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15515664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6411539
X-RAY DIFFRACTIONr_chiral_restr0.0910.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023655
X-RAY DIFFRACTIONr_nbd_refined0.2070.22654
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23284
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2573
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.2113
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.232
X-RAY DIFFRACTIONr_mcbond_it0.6881.52904
X-RAY DIFFRACTIONr_mcangle_it1.11624616
X-RAY DIFFRACTIONr_scbond_it2.09831896
X-RAY DIFFRACTIONr_scangle_it3.4084.51668
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 178 -
Rwork0.245 3488 -
all-3666 -
obs-3666 96.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9787-0.35331.15011.005-0.68633.431-0.0128-0.06310.03240.0268-0.0065-0.0325-0.03540.02590.0193-0.1486-0.01740.0228-0.18510.0039-0.132437.58946.27484.5213
22.2547-0.17460.86331.0743-1.06363.8989-0.02220.21930.1445-0.02560.08450.1070.004-0.0189-0.0623-0.1611-0.01520.0185-0.09630.042-0.121726.7523-7.093331.5441
33.0357-1.11380.04481.62030.41041.45240.05160.11080.1126-0.0892-0.15560.0679-0.0598-0.23860.104-0.133-0.0087-0.0021-0.1059-0.0075-0.154815.6013-8.2248-21.5007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1933 - 192
2X-RAY DIFFRACTION2BB4 - 1903 - 189
3X-RAY DIFFRACTION3CC4 - 1933 - 192

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