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- PDB-5iow: Xanthomonas campestris Peroxiredoxin Q - Structure FFcumene (Hype... -

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Basic information

Entry
Database: PDB / ID: 5iow
TitleXanthomonas campestris Peroxiredoxin Q - Structure FFcumene (Hyperoxidized by cumene hydroperoxide)
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: 1.35 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 ...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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 20, 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)17,2733
Polymers17,2271
Non-polymers462
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.380, 51.370, 40.260
Angle α, β, γ (deg.)90.00, 103.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bacterioferritin comigratory protein


Mass: 17226.607 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 300 K / Method: vapor diffusion
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: 1.35→31.13 Å / Num. obs: 30784 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.37 / Net I/σ(I): 7.4
Reflection shellHighest resolution: 1.35 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2386: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3gkm

3gkm


Resolution: 1.35→29.486 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.38 / Phase error: 29.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 1465 4.76 %Imported from 3gkm
Rwork0.1794 ---
obs0.1817 30722 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→29.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 2 179 1360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081319
X-RAY DIFFRACTIONf_angle_d11805
X-RAY DIFFRACTIONf_dihedral_angle_d22.316474
X-RAY DIFFRACTIONf_chiral_restr0.082202
X-RAY DIFFRACTIONf_plane_restr0.008239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.37330.39381570.41432812X-RAY DIFFRACTION100
1.3733-1.39830.33621030.36092903X-RAY DIFFRACTION100
1.3983-1.42520.3131480.33832929X-RAY DIFFRACTION100
1.4252-1.45430.34451260.34352893X-RAY DIFFRACTION100
1.4543-1.48590.35411480.32832940X-RAY DIFFRACTION100
1.4859-1.52040.38681550.30192782X-RAY DIFFRACTION100
1.5204-1.55850.28761150.27172918X-RAY DIFFRACTION99
1.5585-1.60060.2771330.24592891X-RAY DIFFRACTION100
1.6006-1.64770.29931600.22982846X-RAY DIFFRACTION100
1.6477-1.70090.27931290.21652889X-RAY DIFFRACTION100
1.7009-1.76170.30991680.21282829X-RAY DIFFRACTION99
1.7617-1.83220.27321450.18822904X-RAY DIFFRACTION100
1.8322-1.91560.20731550.18512827X-RAY DIFFRACTION99
1.9156-2.01650.20781340.1552867X-RAY DIFFRACTION99
2.0165-2.14280.20051730.13452830X-RAY DIFFRACTION99
2.1428-2.30820.22231490.14342844X-RAY DIFFRACTION99
2.3082-2.54040.21531410.13732857X-RAY DIFFRACTION99
2.5404-2.90770.16371560.14462865X-RAY DIFFRACTION99
2.9077-3.66230.19411260.13972914X-RAY DIFFRACTION100
3.6623-29.49330.18561470.1512845X-RAY DIFFRACTION100

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