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- PDB-2fy6: Structure of the N-terminal domain of Neisseria meningitidis PilB -

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Basic information

Entry
Database: PDB / ID: 2fy6
TitleStructure of the N-terminal domain of Neisseria meningitidis PilB
ComponentsPeptide methionine sulfoxide reductase msrA/msrB
KeywordsOXIDOREDUCTASE / PILB / Cytochrome maturation protein / Thioredoxin / Methionine sulfoxide reductase
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
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 sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / Mss4-like superfamily / Redoxin / Redoxin ...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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptide methionine sulfoxide reductase MsrA/MsrB
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsRanaivoson, F.M. / Kauffmann, B. / Neiers, F. / Boschi-Muller, S. / Branlant, G. / Favier, F.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The X-ray Structure of the N-terminal Domain of PILB from Neisseria meningitidis Reveals a Thioredoxin-fold
Authors: Ranaivoson, F.M. / Kauffmann, B. / Neiers, F. / Wu, J. / Boschi-Muller, S. / Panjikar, S. / Aubry, A. / Branlant, G. / Favier, F.
History
DepositionFeb 7, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,8844
Polymers15,7171
Non-polymers1673
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.870, 45.169, 59.094
Angle α, β, γ (deg.)90.00, 111.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptide methionine sulfoxide reductase msrA/msrB


Mass: 15716.895 Da / Num. of mol.: 1 / Fragment: thioredoxin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: Z2491 / Gene: msrAB, pilB / Plasmid: pET24c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9JWM8, EC: 1.8.4.6
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 3.5M Ammonium Sulfate, Tris-HCl 50mM pH 8.0, 6mg/mL protein, pH 7.5, microbatch, 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: MARRESEARCH / 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: 1.9→30 Å / Num. obs: 11090 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.084 / Χ2: 0.537 / Net I/σ(I): 6.9
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 100 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1088 / Num. unique obs: 1088 / Χ2: 0.288 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
PDB_EXTRACT1.701data extraction
MAR345data collection
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→18.62 Å / Rfactor Rfree error: 0.007 / FOM work R set: 0.868 / Data cutoff high absF: 585795.812 / 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
Rfree0.219 1099 10.3 %RANDOM
Rwork0.182 ---
all0.205 11087 --
obs0.205 10719 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.635 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å22.13 Å2
2---0.7 Å20 Å2
3----1.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→18.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 0 7 154 1271
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 189 11.2 %
Rwork0.234 1496 -
obs-1685 92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2sulf.parsulf.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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