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- PDB-3hch: Structure of the C-terminal domain (MsrB) of Neisseria meningitid... -

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Basic information

Entry
Database: PDB / ID: 3hch
TitleStructure of the C-terminal domain (MsrB) of Neisseria meningitidis PilB (complex with substrate)
ComponentsPeptide methionine sulfoxide reductase msrA/msrB
KeywordsOXIDOREDUCTASE / PilB / Methionine sulfoxide reductase B / complex with substrate / Disulfide bond / 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 MsrB / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Peptide methionine sulfoxide reductase. / Peptide methionine sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A ...Peptide methionine sulfoxide reductase MsrB / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Peptide methionine sulfoxide reductase. / Peptide methionine sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Beta Complex / Thioredoxin-like superfamily / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Chem-RSM / Peptide methionine sulfoxide reductase MsrA/MsrB
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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: Database references / Derived calculations / Category: database_2 / 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 / _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
B: Peptide methionine sulfoxide reductase msrA/msrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,11912
Polymers32,7322
Non-polymers2,38710
Water2,990166
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A: Peptide methionine sulfoxide reductase msrA/msrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2815
Polymers16,3661
Non-polymers9154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptide methionine sulfoxide reductase msrA/msrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8387
Polymers16,3661
Non-polymers1,4726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.879, 154.879, 154.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Peptide methionine sulfoxide reductase msrA/msrB / Peptide-methionine (R)-S-oxide reductase


Mass: 16366.038 Da / Num. of mol.: 2 / Fragment: MsrB domain (UNP residues 377-522) / Mutation: C440S, C495S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup A (bacteria)
Strain: Z2491 / Gene: msrAB, NMA0290, pilB / Plasmid: pSKPILBMsrB / Production host: Escherichia coli (E. coli) / Strain (production host): BE002
References: UniProt: Q9JWM8, peptide-methionine (R)-S-oxide reductase

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Non-polymers , 5 types, 176 molecules

#2: Chemical ChemComp-RSM / (2S)-2-(acetylamino)-N-methyl-4-[(R)-methylsulfinyl]butanamide


Mass: 220.289 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H16N2O3S
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 4.73 Å3/Da / Density % sol: 73.99 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 8.5
Details: 30 % PEG 400, 0.1M TRIS HCl pH 8.5, 0.2M Na Citrate, 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: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 1, 2004
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 37520 / Num. obs: 37516 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 32.9 % / Rsym value: 0.075 / Net I/σ(I): 28.1
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.428 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MxCuBEdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementStarting model: 3HCG

3hcg


Resolution: 2.1→14.83 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 3.086 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22578 1870 5 %RANDOM
Rwork0.19637 ---
all0.208 37271 --
obs0.19785 35401 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.17 Å2 / Biso mean: 31.686 Å2 / Biso min: 7.56 Å2
Refinement stepCycle: LAST / Resolution: 2.1→14.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 158 166 2594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212582
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6112.0063459
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0525305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09623.388121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48915406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1661517
X-RAY DIFFRACTIONr_chiral_restr0.1320.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021965
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21226
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21720
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2491.51534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12922414
X-RAY DIFFRACTIONr_scbond_it2.72331170
X-RAY DIFFRACTIONr_scangle_it4.2214.51037
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.104→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 136 -
Rwork0.22 2542 -
obs-2542 100 %

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