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- PDB-5im9: Xanthomonas campestris Peroxiredoxin Q - Structure F1 -

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Basic information

Entry
Database: PDB / ID: 5im9
TitleXanthomonas campestris Peroxiredoxin Q - Structure F1
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: 1.1 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 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 9, 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)17,3266
Polymers17,2111
Non-polymers1155
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.560, 51.485, 39.900
Angle α, β, γ (deg.)90.00, 103.51, 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.: 5 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 40.39 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5
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: 0.89014 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: 0.89014 Å / Relative weight: 1
ReflectionResolution: 1.1→51.48 Å / Num. obs: 64661 / % possible obs: 99.1 % / Redundancy: 10.9 % / CC1/2: 0.61 / Net I/σ(I): 12.9
Reflection shellHighest resolution: 1.1 Å

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Processing

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

3gkm


Resolution: 1.1→38.796 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 11.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1382 2683 4.75 %
Rwork0.1161 --
obs0.1171 56386 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→38.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 5 255 1447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081352
X-RAY DIFFRACTIONf_angle_d1.0411859
X-RAY DIFFRACTIONf_dihedral_angle_d20.193498
X-RAY DIFFRACTIONf_chiral_restr0.086210
X-RAY DIFFRACTIONf_plane_restr0.01247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11250.20131710.18853511X-RAY DIFFRACTION98
1.1125-1.12560.20311650.17743422X-RAY DIFFRACTION98
1.1256-1.13930.15221860.16693523X-RAY DIFFRACTION98
1.1393-1.15370.16911760.15543415X-RAY DIFFRACTION98
1.1537-1.16890.17911820.15423474X-RAY DIFFRACTION98
1.1689-1.18490.16071680.14593560X-RAY DIFFRACTION99
1.1849-1.20190.18321780.14233456X-RAY DIFFRACTION98
1.2019-1.21980.16961670.13253467X-RAY DIFFRACTION98
1.2198-1.23890.14011650.12563523X-RAY DIFFRACTION99
1.2389-1.25920.14491660.12383505X-RAY DIFFRACTION98
1.2592-1.28090.15661910.11723505X-RAY DIFFRACTION99
1.2809-1.30420.14861730.10933469X-RAY DIFFRACTION99
1.3042-1.32930.14141860.10643570X-RAY DIFFRACTION99
1.3293-1.35640.12541460.10083497X-RAY DIFFRACTION99
1.3564-1.38590.14021600.0993519X-RAY DIFFRACTION99
1.3859-1.41810.10151760.0913604X-RAY DIFFRACTION99
1.4181-1.45360.12551630.08683481X-RAY DIFFRACTION99
1.4536-1.49290.11741700.08543524X-RAY DIFFRACTION100
1.4929-1.53680.10871760.07853545X-RAY DIFFRACTION100
1.5368-1.58650.10541570.07993535X-RAY DIFFRACTION100
1.5865-1.64320.11661920.08643538X-RAY DIFFRACTION100
1.6432-1.70890.10881710.08683516X-RAY DIFFRACTION100
1.7089-1.78670.1141860.09413595X-RAY DIFFRACTION100
1.7867-1.88090.12211860.10153532X-RAY DIFFRACTION100
1.8809-1.99880.12251810.10033544X-RAY DIFFRACTION100
1.9988-2.15310.13182100.10123496X-RAY DIFFRACTION100
2.1531-2.36970.12981720.11153595X-RAY DIFFRACTION100
2.3697-2.71250.15182040.12573519X-RAY DIFFRACTION100
2.7125-3.41720.15571540.13523544X-RAY DIFFRACTION100
3.4172-38.820.14321830.13743505X-RAY DIFFRACTION99

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