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- PDB-5ipg: Xanthomonas campestris Peroxiredoxin Q - Structure FFT-butyl (Hyp... -

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Basic information

Entry
Database: PDB / ID: 5ipg
TitleXanthomonas campestris Peroxiredoxin Q - Structure FFT-butyl (Hyperoxodized by t-butyl 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterioferritin comigratory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3943
Polymers17,3481
Non-polymers462
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.430, 51.450, 40.310
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: 17347.768 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.: 178 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
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→39.19 Å / Num. obs: 30350 / % possible obs: 97.8 % / Redundancy: 7.1 % / CC1/2: 0.333 / Net I/σ(I): 10.7
Reflection shellHighest resolution: 1.35 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: 1.35→34.449 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 22.38
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 1460 4.79 %Imported from 3gkm
Rwork0.1627 ---
obs0.164 30350 97.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→34.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 2 178 1355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151350
X-RAY DIFFRACTIONf_angle_d1.5981852
X-RAY DIFFRACTIONf_dihedral_angle_d16.448489
X-RAY DIFFRACTIONf_chiral_restr0.079205
X-RAY DIFFRACTIONf_plane_restr0.009249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.37330.29611510.32952780X-RAY DIFFRACTION97
1.3733-1.39830.35161120.30722853X-RAY DIFFRACTION97
1.3983-1.42520.3341340.29812829X-RAY DIFFRACTION97
1.4252-1.45430.31911220.27882807X-RAY DIFFRACTION97
1.4543-1.48590.29451510.26192860X-RAY DIFFRACTION98
1.4859-1.52050.28661550.23272738X-RAY DIFFRACTION97
1.5205-1.55850.19641150.21122840X-RAY DIFFRACTION97
1.5585-1.60060.25191360.20132822X-RAY DIFFRACTION98
1.6006-1.64770.24981520.19312823X-RAY DIFFRACTION98
1.6477-1.70090.20331340.17692848X-RAY DIFFRACTION98
1.7009-1.76170.19941680.16072792X-RAY DIFFRACTION98
1.7617-1.83220.18441400.1542879X-RAY DIFFRACTION98
1.8322-1.91560.20061540.15672820X-RAY DIFFRACTION99
1.9156-2.01660.151340.14532833X-RAY DIFFRACTION98
2.0166-2.14290.19491750.13452838X-RAY DIFFRACTION99
2.1429-2.30830.1951510.1372855X-RAY DIFFRACTION99
2.3083-2.54060.19411380.14472880X-RAY DIFFRACTION99
2.5406-2.9080.17131550.15882836X-RAY DIFFRACTION98
2.908-3.66310.16881270.15022890X-RAY DIFFRACTION99
3.6631-34.46050.15551490.14372833X-RAY DIFFRACTION99

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