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- PDB-3gkn: Insights into the Alkyl Peroxide Reduction Activity of Xanthomona... -

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Basic information

Entry
Database: PDB / ID: 3gkn
TitleInsights into the Alkyl Peroxide Reduction Activity of Xanthomonas campestris Bacterioferritin Comigratory Protein from the Trapped Intermediate/Ligand Complex Structures
ComponentsBacterioferritin comigratory protein
KeywordsOXIDOREDUCTASE / Xanthomonas campestris / Bcp / Prx / Atypical 2-Cys
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
NAPHTHALENE-2,6-DISULFONIC ACID / Peroxiredoxin Bcp
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsLiao, S.-J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Insights into the alkyl peroxide reduction pathway of Xanthomonas campestris bacterioferritin comigratory protein from the trapped intermediate-ligand complex structures
Authors: Liao, S.-J. / Yang, C.-Y. / Chin, K.-H. / Wang, A.H.-J. / Chou, S.-H.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 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
B: Bacterioferritin comigratory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,78516
Polymers35,0802
Non-polymers1,70614
Water6,593366
1
A: Bacterioferritin comigratory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4819
Polymers17,5401
Non-polymers9418
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacterioferritin comigratory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3057
Polymers17,5401
Non-polymers7656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.110, 56.490, 74.900
Angle α, β, γ (deg.)90.00, 119.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bacterioferritin comigratory protein


Mass: 17539.963 Da / Num. of mol.: 2 / Mutation: C48A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: 17 / Gene: BCP / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8P9V9, peroxiredoxin
#2: Chemical ChemComp-BIH / NAPHTHALENE-2,6-DISULFONIC ACID / 2,6-NAPHTHALENEDISULFONIC ACID / 2,6-NAPHTHALENEDISULPHONIC ACID


Mass: 288.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O6S2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 1.7M (NH4)2SO4, 0.2M NaCl, 0.1M Na cacodylate pH 6.5, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 60047 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 25.58
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 2 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.16 / Rsym value: 0.426 / % possible all: 92.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GKK

3gkk


Resolution: 1.47→24.88 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2856 4.6 %RANDOM
Rwork0.198 ---
obs0.198 54389 91.5 %-
all-57245 --
Solvent computationBsol: 55.918 Å2
Displacement parametersBiso mean: 21.094 Å2
Baniso -1Baniso -2Baniso -3
1-2.128 Å20 Å2-1.005 Å2
2---0.524 Å20 Å2
3----1.604 Å2
Refinement stepCycle: LAST / Resolution: 1.47→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 102 366 2846
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.238
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.47→1.52 Å / % reflection Rfree: 5 % / % reflection obs: 92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3NDAD_GC_PAR.TXTNDAD_GC_TOP.TXT

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