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- PDB-5imd: Xanthomonas campestris Peroxiredoxin Q - Structure F4 -

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Basic information

Entry
Database: PDB / ID: 5imd
TitleXanthomonas campestris Peroxiredoxin Q - Structure F4
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 / OXYGEN ATOM / Peroxiredoxin Bcp
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 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 13, 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)17,3355
Polymers17,2271
Non-polymers1084
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.660, 51.510, 40.060
Angle α, β, γ (deg.)90.00, 104.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bacterioferritin comigratory protein


Mass: 17226.607 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: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
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: 1.16→25.75 Å / Num. obs: 46092 / % possible obs: 94.7 % / Redundancy: 3.2 % / CC1/2: 0.85 / Net I/σ(I): 6.4
Reflection shellHighest resolution: 1.16 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: 1.16→21.152 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 17.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1719 2187 4.74 %
Rwork0.1436 --
obs0.1449 46047 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.16→21.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 6 306 1508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141426
X-RAY DIFFRACTIONf_angle_d1.6921956
X-RAY DIFFRACTIONf_dihedral_angle_d22.379530
X-RAY DIFFRACTIONf_chiral_restr0.105215
X-RAY DIFFRACTIONf_plane_restr0.02263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.17320.2559950.19861748X-RAY DIFFRACTION59
1.1732-1.1870.2361840.18921969X-RAY DIFFRACTION65
1.187-1.20150.20131130.18282178X-RAY DIFFRACTION71
1.2015-1.21670.19881000.18042288X-RAY DIFFRACTION75
1.2167-1.23270.24491340.18912617X-RAY DIFFRACTION86
1.2327-1.24960.20491240.18852897X-RAY DIFFRACTION96
1.2496-1.26740.2171720.20093033X-RAY DIFFRACTION100
1.2674-1.28640.2391480.20573034X-RAY DIFFRACTION100
1.2864-1.30650.27191480.18293033X-RAY DIFFRACTION100
1.3065-1.32790.26381620.16783044X-RAY DIFFRACTION100
1.3279-1.35080.15441300.15092983X-RAY DIFFRACTION100
1.3508-1.37530.17661510.16023105X-RAY DIFFRACTION100
1.3753-1.40180.18791330.14023052X-RAY DIFFRACTION100
1.4018-1.43040.17381430.14873051X-RAY DIFFRACTION100
1.4304-1.46150.1991460.15373023X-RAY DIFFRACTION100
1.4615-1.49550.18151450.14863035X-RAY DIFFRACTION100
1.4955-1.53290.19541510.143025X-RAY DIFFRACTION100
1.5329-1.57430.13551350.13163059X-RAY DIFFRACTION100
1.5743-1.62060.15331540.12583070X-RAY DIFFRACTION100
1.6206-1.67290.19391570.12213036X-RAY DIFFRACTION100
1.6729-1.73260.1551710.12373004X-RAY DIFFRACTION100
1.7326-1.8020.14951370.12023044X-RAY DIFFRACTION100
1.802-1.88390.16191660.13563029X-RAY DIFFRACTION100
1.8839-1.98320.17791610.15353040X-RAY DIFFRACTION100
1.9832-2.10730.1341810.11382984X-RAY DIFFRACTION100
2.1073-2.26990.16681510.14772991X-RAY DIFFRACTION99
2.2699-2.4980.16421440.12573054X-RAY DIFFRACTION100
2.498-2.85870.14941820.13413005X-RAY DIFFRACTION100
2.8587-3.59880.13911280.12733045X-RAY DIFFRACTION99
3.5988-21.15590.16521470.14392840X-RAY DIFFRACTION94

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