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- PDB-3bqf: Structure of the central domain (MsrA) of Neisseria meningitidis ... -

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Basic information

Entry
Database: PDB / ID: 3bqf
TitleStructure of the central domain (MsrA) of Neisseria meningitidis PilB (complex with a substrate)
ComponentsPeptide methionine sulfoxide reductase msrA/msrB
KeywordsOXIDOREDUCTASE / PILB / Methionine sulfoxide reductase A / complex with a substrate / Electron transport / Multifunctional enzyme / Redox-active center / Transport
Function / homology
Function and homology information


L-methionine:thioredoxin-disulfide S-oxidoreductase activity / peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein repair / protein modification process / response to oxidative stress / cytoplasm
Similarity search - Function
Peptide Methionine Sulfoxide Reductase; Chain A / Peptide methionine sulphoxide reductase MsrA / Peptide methionine sulfoxide reductase MsrB / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Peptide methionine sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / Mss4-like superfamily ...Peptide Methionine Sulfoxide Reductase; Chain A / Peptide methionine sulphoxide reductase MsrA / Peptide methionine sulfoxide reductase MsrB / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Peptide methionine sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / Mss4-like superfamily / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-SSM / Peptide methionine sulfoxide reductase MsrA/MsrB
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsRanaivoson, F.M. / Kauffmann, B. / Favier, F.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: A structural analysis of the catalytic mechanism of methionine sulfoxide reductase A from Neisseria meningitidis
Authors: Ranaivoson, F.M. / Antoine, M. / Kauffmann, B. / Boschi-Muller, S. / Aubry, A. / Branlant, G. / Favier, F.
History
DepositionDec 20, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide methionine sulfoxide reductase msrA/msrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1292
Polymers21,9081
Non-polymers2201
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.933, 50.305, 66.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptide methionine sulfoxide reductase msrA/msrB / PILB


Mass: 21908.264 Da / Num. of mol.: 1
Fragment: Msra Domain, Peptide methionine sulfoxide reductase A, UNP residues 196-389
Mutation: C207S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: Z2491 / Gene: pilB / Plasmid: pSKPILBMsrA / Production host: Escherichia coli (E. coli) / Strain (production host): BE002
References: UniProt: Q9JWM8, peptide-methionine (S)-S-oxide reductase
#2: Chemical ChemComp-SSM / (2S)-2-(acetylamino)-N-methyl-4-[(S)-methylsulfinyl]butanamide


Mass: 220.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 1.679566 Å3/Da / Density % sol: 26.766775 %
Crystal growTemperature: 293 K / Method: microbatch-under-oil / pH: 9
Details: 1 volume of 30% PEG 550 MME, 0.1M Bicine pH 9.0, 0.1M NaCl, mixed with 1 volume of 50mM TRIS HCl, 2mM EDTA pH 8, 18mg/mL protein + 200mM AcMet(R,S)SONHMe, microbatch-under-oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 15, 2003 / Details: Bent Mirror
RadiationMonochromator: Triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.22→20 Å / Num. all: 7685 / Num. obs: 7491 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.3
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4.24 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
CNS1refinement
PDB_EXTRACT3.004data extraction
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BQE

3bqe


Resolution: 2.24→19.8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 458280.406 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 694 9.7 %RANDOM
Rwork0.185 ---
all-7475 --
obs-7169 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.551 Å2 / ksol: 0.479 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2---0.93 Å20 Å2
3----0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.24→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1341 0 14 82 1437
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it1.592
X-RAY DIFFRACTIONc_scangle_it2.362.5
LS refinement shellResolution: 2.24→2.38 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 113 9.8 %
Rwork0.213 1041 -
all-1154 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3S_mso.paramS_mso.top

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