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- PDB-5imc: Xanthomonas campestris Peroxiredoxin Q - Structure F3 -

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Basic information

Entry
Database: PDB / ID: 5imc
TitleXanthomonas campestris Peroxiredoxin Q - Structure F3
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
FORMIC ACID / Peroxiredoxin Bcp
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 6, 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
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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3034
Polymers17,2111
Non-polymers923
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-21 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.530, 51.240, 40.010
Angle α, β, γ (deg.)90.00, 103.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bacterioferritin comigratory protein


Mass: 17210.609 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: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.08 Å3/Da / Density % sol: 41 %
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: 0.97648 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: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.05→10.55 Å / Num. obs: 56804 / % possible obs: 87.6 % / Redundancy: 6.6 % / CC1/2: 0.718 / Net I/σ(I): 15.8
Reflection shellHighest resolution: 1.05 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: 1.05→10.55 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 15.29
RfactorNum. reflection% reflectionSelection details
Rfree0.1435 2694 4.74 %Imported from 3gkm
Rwork0.125 ---
obs0.1259 56804 87.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.05→10.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 5 288 1483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151406
X-RAY DIFFRACTIONf_angle_d1.9721927
X-RAY DIFFRACTIONf_dihedral_angle_d14.323522
X-RAY DIFFRACTIONf_chiral_restr0.097213
X-RAY DIFFRACTIONf_plane_restr0.021258
LS refinement shellResolution: 1.05→1.0619 Å
RfactorNum. reflection% reflection
Rfree0.6409 76 -
Rwork0.4877 3845 -
obs--95 %

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