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

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Basic information

Entry
Database: PDB / ID: 3bqe
TitleStructure of the central domain (MsrA) of Neisseria meningitidis PilB (reduced form)
ComponentsPeptide methionine sulfoxide reductase msrA/msrB
KeywordsOXIDOREDUCTASE / PILB / Methionine sulfoxide reductase A / reduced form / 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
Peptide methionine sulfoxide reductase MsrA/MsrB
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide methionine sulfoxide reductase msrA/msrB


Theoretical massNumber of molelcules
Total (without water)21,9241
Polymers21,9241
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.488, 49.183, 66.153
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: 21924.328 Da / Num. of mol.: 1
Fragment: MsrA domain, Peptide methionine sulfoxide reductase A, UNP residues 196-389
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.61562 Å3/Da / Density % sol: 23.868227 %
Crystal growTemperature: 293 K / Method: microbatch-under-oil / pH: 7.5
Details: 1 volume of 20% PEG 8000, 0.1M Na HEPES pH 7.5, mixed with 1 volume of 50mM TRIS HCl, 2mM EDTA pH 8, 18mg/mL protein, microbatch-under-oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Feb 10, 2000
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 10048 / Num. obs: 9614 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.04 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.98 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.3 / % possible all: 90.2

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Processing

Software
NameVersionClassificationNB
CNS1refinement
PDB_EXTRACT3.004data extraction
XPRESS(Mac Science)data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NWA

1nwa


Resolution: 2→16.54 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 123286.25 / 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
Rfree0.203 469 5 %RANDOM
Rwork0.175 ---
all-10045 --
obs-9342 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.617 Å2 / ksol: 0.453 e/Å3
Displacement parametersBiso mean: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--3.52 Å20 Å2
3----4.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→16.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 0 146 1503
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it2.912
X-RAY DIFFRACTIONc_scangle_it3.872.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 67 4.7 %
Rwork0.221 1346 -
all-1413 -
obs--86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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