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- PDB-2h30: Crystal structure of the N-terminal domain of PilB from Neisseria... -

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Basic information

Entry
Database: PDB / ID: 2h30
TitleCrystal structure of the N-terminal domain of PilB from Neisseria gonorrhoeae
ComponentsPeptide methionine sulfoxide reductase msrA/msrB
KeywordsOXIDOREDUCTASE / reduced / methionine sulfoxide / thiol-disulfide exchange
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 gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsBrot, N. / Collet, J.F. / Johnson, L.C. / Jonsson, T.J. / Weissbach, H. / Lowther, W.T.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Thioredoxin Domain of Neisseria gonorrhoeae PilB Can Use Electrons from DsbD to Reduce Downstream Methionine Sulfoxide Reductases.
Authors: Brot, N. / Collet, J.F. / Johnson, L.C. / Jonsson, T.J. / Weissbach, H. / Lowther, W.T.
History
DepositionMay 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)17,9241
Polymers17,9241
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.381, 51.421, 80.396
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 / Thioredoxin / Peptide methionine sulfoxide reductase msrA (Protein-methionine-S-oxide reductase) ...Thioredoxin / Peptide methionine sulfoxide reductase msrA (Protein-methionine-S-oxide reductase) (Peptide Met(O) reductase) / Peptide methionine sulfoxide reductase msrB


Mass: 17924.131 Da / Num. of mol.: 1 / Fragment: N-terminal domain / Mutation: L38M, L41M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: msrAB, pilB / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)gold / References: UniProt: P14930, EC: 1.8.4.6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Equal volumes of protein (30 mg mL-1 in 20 mM Hepes pH 7.5, 100 mM NaCl) and well solutions (0.1 M Mes pH 6.5, 0.2 M NH4SO4, 26% PEG 2000 MME), VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9790,0.9791,0.9500
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2003
RadiationMonochromator: Double silicon crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97911
30.951
ReflectionResolution: 1.6→33.1 Å / Num. obs: 24399 / % possible obs: 99.3 % / Observed criterion σ(I): 7.9 / Redundancy: 6.7 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 25
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 7.9 / % possible all: 98.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
d*TREKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→33 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.227 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1235 5.1 %RANDOM
Rwork0.188 ---
all0.189 ---
obs-24212 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.103 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.8 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 0 90 1256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221195
X-RAY DIFFRACTIONr_angle_refined_deg1.851.9541625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2915150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45825.31947
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24215202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.589153
X-RAY DIFFRACTIONr_chiral_restr0.1360.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02895
X-RAY DIFFRACTIONr_nbd_refined0.2170.2534
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.212
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.26
X-RAY DIFFRACTIONr_mcbond_it1.4521.5765
X-RAY DIFFRACTIONr_mcangle_it2.29421212
X-RAY DIFFRACTIONr_scbond_it3.3183497
X-RAY DIFFRACTIONr_scangle_it5.0814.5413
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 96 -
Rwork0.193 1654 -
obs-1750 98.93 %

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