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- PDB-3hci: Structure of MsrB from Xanthomonas campestris (complex-like form) -

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Basic information

Entry
Database: PDB / ID: 3hci
TitleStructure of MsrB from Xanthomonas campestris (complex-like form)
ComponentsPeptide methionine sulfoxide reductase
KeywordsOXIDOREDUCTASE / Methionine sulfoxide reductase B / Xanthomonas campestris / complex with substrate
Function / homology
Function and homology information


peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / protein repair / response to oxidative stress / zinc ion binding / cytoplasm
Similarity search - Function
Peptide methionine sulfoxide reductase MsrB / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Peptide methionine sulfoxide reductase. / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-RSM / Peptide methionine sulfoxide reductase MsrB / Peptide methionine sulfoxide reductase MsrB
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.59 Å
AuthorsRanaivoson, F.M. / Kauffmann, B. / Favier, F.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Methionine sulfoxide reductase B displays a high level of flexibility.
Authors: Ranaivoson, F.M. / Neiers, F. / Kauffmann, B. / Boschi-Muller, S. / Branlant, G. / Favier, F.
History
DepositionMay 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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: Peptide methionine sulfoxide reductase
B: Peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0436
Polymers33,6522
Non-polymers3914
Water1,72996
1
A: Peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1113
Polymers16,8261
Non-polymers2862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9313
Polymers16,8261
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.436, 74.203, 122.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptide methionine sulfoxide reductase / MsrB


Mass: 16825.787 Da / Num. of mol.: 2 / Mutation: C125S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: msrb, xcc-b100_3837 / Plasmid: pSKMsrBXc / Production host: Escherichia coli (E. coli) / Strain (production host): BE002
References: UniProt: B0RWG5, UniProt: Q8P4Q6*PLUS, peptide-methionine (S)-S-oxide reductase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-RSM / (2S)-2-(acetylamino)-N-methyl-4-[(R)-methylsulfinyl]butanamide


Mass: 220.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16N2O3S
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 7.5
Details: 18 % PEG 8000, 0.1M Na HEPES pH 7.5, 0.2M, 0.05M TRIS HCl pH 8 , microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.24 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 14, 2005
RadiationMonochromator: Fixed exit double crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. all: 11793 / Num. obs: 11522 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.03 % / Rsym value: 0.093 / Net I/σ(I): 10.9
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.333 / % possible all: 92

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Processing

Software
NameVersionClassification
DENZOdata reduction
MOLREPphasing
REFMAC5.2.0019refinement
SCALEPACKdata scaling
RefinementStarting model: 3HCG

3hcg


Resolution: 2.59→24.25 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.888 / SU B: 10.492 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.794 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24737 543 4.7 %RANDOM
Rwork0.19588 ---
all0.215 11822 --
obs0.19837 10912 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.396 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.36 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.59→24.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 17 96 2463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212433
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.9733320
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6285304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50923.276116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06615344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4681520
X-RAY DIFFRACTIONr_chiral_restr0.0690.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021959
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.21068
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21619
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2129
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0460.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2981.51579
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.55622489
X-RAY DIFFRACTIONr_scbond_it0.7283942
X-RAY DIFFRACTIONr_scangle_it1.284.5831
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.591→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 28 -
Rwork0.31 686 -
obs--83.41 %

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