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- PDB-5iiz: Xanthomonas campestris Peroxiredoxin Q - Structure F0 -

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Basic information

Entry
Database: PDB / ID: 5iiz
TitleXanthomonas campestris Peroxiredoxin Q - Structure F0
ComponentsBacterioferritin comigratory protein
KeywordsOXIDOREDUCTASE / PrxQ / BCP / Peroxidase / redox
Function / homology
Function and homology information


antioxidant activity / oxidoreductase activity
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
Bacterioferritin comigratory protein
Similarity search - Component
Biological speciesXanthomonas campestris pv. raphani 756C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsPerkins, A. / Parsonage, D. / Nelson, K.J. / Poole, L.B. / Karplus, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
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 1, 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, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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
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_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details

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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)17,3106
Polymers17,1951
Non-polymers1155
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.400, 51.360, 39.955
Angle α, β, γ (deg.)90.00, 103.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bacterioferritin comigratory protein


Mass: 17194.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. raphani 756C (bacteria)
Gene: bcp, XCR_1978 / Production host: Escherichia coli (E. coli) / References: UniProt: G0CBC0
#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.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.62 %
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: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.89014 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89014 Å / Relative weight: 1
ReflectionResolution: 1.05→35 Å / Num. obs: 63833 / % possible obs: 98 % / Redundancy: 7 % / CC1/2: 0.7 / Net I/σ(I): 11.8
Reflection shellHighest resolution: 1.05 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: 1.05→34.455 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 15.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1534 3019 4.73 %
Rwork0.1349 --
obs0.1358 63833 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→34.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1189 0 5 230 1424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071348
X-RAY DIFFRACTIONf_angle_d1.0271851
X-RAY DIFFRACTIONf_dihedral_angle_d19.669493
X-RAY DIFFRACTIONf_chiral_restr0.088209
X-RAY DIFFRACTIONf_plane_restr0.009246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.06190.38972000.3513866X-RAY DIFFRACTION97
1.0619-1.07440.31451640.32764001X-RAY DIFFRACTION96
1.0744-1.08750.29921860.2833913X-RAY DIFFRACTION97
1.0875-1.10130.28811980.273945X-RAY DIFFRACTION97
1.1013-1.11580.28532090.24433922X-RAY DIFFRACTION97
1.1158-1.13110.24141950.21423901X-RAY DIFFRACTION97
1.1311-1.14720.20252040.20563918X-RAY DIFFRACTION97
1.1472-1.16440.20471950.18863938X-RAY DIFFRACTION97
1.1644-1.18260.18972020.17534024X-RAY DIFFRACTION98
1.1826-1.20190.19721940.15563961X-RAY DIFFRACTION98
1.2019-1.22270.14561860.13013970X-RAY DIFFRACTION97
1.2227-1.24490.14351860.12253977X-RAY DIFFRACTION98
1.2449-1.26880.13482080.11654002X-RAY DIFFRACTION98
1.2688-1.29480.13442060.10243918X-RAY DIFFRACTION98
1.2948-1.32290.12132110.09783964X-RAY DIFFRACTION98
1.3229-1.35370.14181680.09414075X-RAY DIFFRACTION98
1.3537-1.38750.12011750.09384036X-RAY DIFFRACTION98
1.3875-1.4250.12332010.09533998X-RAY DIFFRACTION99
1.425-1.4670.12662030.09854016X-RAY DIFFRACTION99
1.467-1.51430.12611990.09564015X-RAY DIFFRACTION99
1.5143-1.56850.11161730.09144013X-RAY DIFFRACTION99
1.5685-1.63130.10971920.09674057X-RAY DIFFRACTION99
1.6313-1.70550.12542200.10374024X-RAY DIFFRACTION99
1.7055-1.79540.14581990.11144038X-RAY DIFFRACTION99
1.7954-1.90790.13592310.11644055X-RAY DIFFRACTION100
1.9079-2.05520.12772040.1214028X-RAY DIFFRACTION100
2.0552-2.2620.14852360.11734017X-RAY DIFFRACTION100
2.262-2.58920.132060.12924060X-RAY DIFFRACTION100
2.5892-3.26170.15171800.14884100X-RAY DIFFRACTION100
3.2617-34.47310.17332100.1533950X-RAY DIFFRACTION98

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