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- PDB-5iph: Xanthomonas campestris Peroxiredoxin Q - C84S mutant -

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Basic information

Entry
Database: PDB / ID: 5iph
TitleXanthomonas campestris Peroxiredoxin Q - C84S 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
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 9, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)17,2022
Polymers17,1791
Non-polymers231
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.304, 50.797, 39.486
Angle α, β, γ (deg.)90.00, 103.59, 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: C84S
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.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 35% PEG 4000, 0.1 M sodium acetate pH 5.5, 1 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→38.38 Å / Num. obs: 33454 / % possible obs: 100 % / Redundancy: 8.9 % / CC1/2: 0.391 / Net I/σ(I): 5.6
Reflection shellHighest resolution: 1.3 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: 1.3→34.316 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 23.51
RfactorNum. reflection% reflectionSelection details
Rfree0.2061 1593 4.75 %Imported from 3gkm
Rwork0.168 ---
obs0.1699 33454 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→34.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 1 237 1432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091333
X-RAY DIFFRACTIONf_angle_d1.2451825
X-RAY DIFFRACTIONf_dihedral_angle_d14.472485
X-RAY DIFFRACTIONf_chiral_restr0.053205
X-RAY DIFFRACTIONf_plane_restr0.02242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.32030.43521440.43332831X-RAY DIFFRACTION99
1.3203-1.3420.49331320.4052828X-RAY DIFFRACTION100
1.342-1.36510.42661180.37462879X-RAY DIFFRACTION100
1.3651-1.38990.36551390.3352717X-RAY DIFFRACTION100
1.3899-1.41670.27121350.29212953X-RAY DIFFRACTION100
1.4167-1.44560.34531260.25772810X-RAY DIFFRACTION100
1.4456-1.4770.2791500.24862854X-RAY DIFFRACTION100
1.477-1.51140.2841450.22722833X-RAY DIFFRACTION100
1.5114-1.54920.2271170.2162855X-RAY DIFFRACTION100
1.5492-1.59110.26071430.20882841X-RAY DIFFRACTION100
1.5911-1.63790.25531420.19682828X-RAY DIFFRACTION100
1.6379-1.69070.20881490.16422818X-RAY DIFFRACTION100
1.6907-1.75120.19741540.14292831X-RAY DIFFRACTION100
1.7512-1.82130.18051400.14312842X-RAY DIFFRACTION100
1.8213-1.90420.17111530.13492818X-RAY DIFFRACTION100
1.9042-2.00450.15891390.12512865X-RAY DIFFRACTION100
2.0045-2.13010.1811740.12462793X-RAY DIFFRACTION100
2.1301-2.29450.16151400.13382877X-RAY DIFFRACTION100
2.2945-2.52540.1871600.13752815X-RAY DIFFRACTION100
2.5254-2.89070.19371390.14772817X-RAY DIFFRACTION100
2.8907-3.64130.17891270.14322878X-RAY DIFFRACTION100
3.6413-34.32750.1641470.13892817X-RAY DIFFRACTION100

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