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- PDB-5io2: Xanthomonas campestris Peroxiredoxin Q - C48S mutant -

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Basic information

Entry
Database: PDB / ID: 5io2
TitleXanthomonas campestris Peroxiredoxin Q - C48S mutant
ComponentsBacterioferritin comigratory protein
KeywordsOXIDOREDUCTASE / PrxQ / BCP / Peroxidase / redox
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / cellular response to oxidative stress / cytoplasm
Similarity search - Function
Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Peroxiredoxin Bcp
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsPerkins, A. / Parsonage, D. / Nelson, K.J. / Poole, L.B. / Karplus, A.
CitationJournal: Structure / Year: 2016
Title: Peroxiredoxin Catalysis at Atomic Resolution.
Authors: Perkins, A. / Parsonage, D. / Nelson, K.J. / Ogba, O.M. / Cheong, P.H. / Poole, L.B. / Karplus, P.A.
History
DepositionMar 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterioferritin comigratory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3194
Polymers17,1791
Non-polymers1413
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.630, 51.280, 39.680
Angle α, β, γ (deg.)90.00, 103.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bacterioferritin comigratory protein


Mass: 17178.543 Da / Num. of mol.: 1 / Mutation: C48S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25) (bacteria)
Strain: ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25 / Gene: XCC1738 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8P9V9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 4000, 0.1 M sodium acetate pH 5.5, 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.2→30.81 Å / Num. obs: 37466 / % possible obs: 86.4 % / Redundancy: 3.6 % / CC1/2: 0.707 / Net I/σ(I): 8.4
Reflection shellHighest resolution: 1.2 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2006: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3gkm

3gkm


Resolution: 1.2→29.477 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 18.12
RfactorNum. reflection% reflection
Rfree0.1666 1771 4.71 %
Rwork0.1387 --
obs0.14 37466 86.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.2→29.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 7 320 1522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121339
X-RAY DIFFRACTIONf_angle_d1.271838
X-RAY DIFFRACTIONf_dihedral_angle_d13.503484
X-RAY DIFFRACTIONf_chiral_restr0.074208
X-RAY DIFFRACTIONf_plane_restr0.018243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.21650.276600.25011290X-RAY DIFFRACTION40
1.2165-1.23380.261620.24531472X-RAY DIFFRACTION44
1.2338-1.25230.287840.24151704X-RAY DIFFRACTION52
1.2523-1.27180.2412860.23261914X-RAY DIFFRACTION58
1.2718-1.29270.32551200.23092114X-RAY DIFFRACTION66
1.2927-1.3150.26531060.232395X-RAY DIFFRACTION74
1.315-1.33890.22361270.22542827X-RAY DIFFRACTION88
1.3389-1.36460.23951470.21153145X-RAY DIFFRACTION95
1.3646-1.39250.27671330.19473099X-RAY DIFFRACTION94
1.3925-1.42280.21281400.18443125X-RAY DIFFRACTION95
1.4228-1.45590.19181470.16763105X-RAY DIFFRACTION96
1.4559-1.49230.21191560.16143071X-RAY DIFFRACTION95
1.4923-1.53260.19781650.14413120X-RAY DIFFRACTION96
1.5326-1.57770.15191310.14433145X-RAY DIFFRACTION96
1.5777-1.62860.18361680.14143085X-RAY DIFFRACTION96
1.6286-1.68680.16491590.143162X-RAY DIFFRACTION96
1.6868-1.75440.16451740.13293110X-RAY DIFFRACTION96
1.7544-1.83420.16751600.12373120X-RAY DIFFRACTION97
1.8342-1.93090.16171650.11363176X-RAY DIFFRACTION98
1.9309-2.05180.15791690.11033159X-RAY DIFFRACTION97
2.0518-2.21020.10941850.10283177X-RAY DIFFRACTION98
2.2102-2.43250.13971410.11493167X-RAY DIFFRACTION98
2.4325-2.78430.14251900.12633182X-RAY DIFFRACTION98
2.7843-3.5070.14991350.12453177X-RAY DIFFRACTION97
3.507-29.48590.1411650.1223208X-RAY DIFFRACTION99

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