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- PDB-3e0o: Crystal structure of MsrB -

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Basic information

Entry
Database: PDB / ID: 3e0o
TitleCrystal structure of MsrB
ComponentsPeptide methionine sulfoxide reductase msrB
KeywordsOXIDOREDUCTASE / msrB
Function / homology
Function and homology information


peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / protein repair / 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. / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Peptide methionine sulfoxide reductase MsrB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsPark, A.K. / Shin, Y.J. / Kim, Y.K. / Chi, Y.M. / Hwang, K.Y.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Structural and Kinetic Analysis of an MsrA-MsrB Fusion Protein from Streptococcus pneumoniae
Authors: Kim, Y.K. / Shin, Y.J. / Lee, W.-H. / Kim, H.-Y. / Hwang, K.Y.
History
DepositionJul 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 msrB
B: Peptide methionine sulfoxide reductase msrB
C: Peptide methionine sulfoxide reductase msrB
D: Peptide methionine sulfoxide reductase msrB
E: Peptide methionine sulfoxide reductase msrB
F: Peptide methionine sulfoxide reductase msrB


Theoretical massNumber of molelcules
Total (without water)100,5466
Polymers100,5466
Non-polymers00
Water6,972387
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptide methionine sulfoxide reductase msrB


Theoretical massNumber of molelcules
Total (without water)16,7581
Polymers16,7581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Peptide methionine sulfoxide reductase msrB


Theoretical massNumber of molelcules
Total (without water)16,7581
Polymers16,7581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Peptide methionine sulfoxide reductase msrB


Theoretical massNumber of molelcules
Total (without water)16,7581
Polymers16,7581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Peptide methionine sulfoxide reductase msrB


Theoretical massNumber of molelcules
Total (without water)16,7581
Polymers16,7581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: Peptide methionine sulfoxide reductase msrB


Theoretical massNumber of molelcules
Total (without water)16,7581
Polymers16,7581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
F: Peptide methionine sulfoxide reductase msrB


Theoretical massNumber of molelcules
Total (without water)16,7581
Polymers16,7581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.114, 136.114, 61.925
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

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


Mass: 16757.732 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: msrB, yppQ, BSU21680 / Plasmid: pET 22b / Production host: Escherichia coli (E. coli)
References: UniProt: P54155, peptide-methionine (R)-S-oxide reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 20

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 1.2M Lithium sulfate, 0.1M HEPES, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A10.97182
SYNCHROTRONPAL/PLS 4A20.97950,0.97962,0.97182
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDJun 22, 2007wiggler
ADSC QUANTUM 2102CCDJun 22, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1wigglerSINGLE WAVELENGTHMx-ray1
2SeMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.971821
20.97951
30.979621
ReflectionResolution: 2.6→45.8 Å / Num. all: 39435 / Num. obs: 39083 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.4 Å2 / Limit h max: 45 / Limit h min: -44 / Limit k max: 52 / Limit k min: -44 / Limit l max: 23 / Limit l min: 0 / Observed criterion F max: 32858.3 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.5
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3846 / % possible all: 97.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→19.79 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 32859.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.294 3885 10 %RANDOM
Rwork0.235 ---
obs0.235 38752 98.2 %-
all-38836 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.7344 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20 Å20 Å2
2--2.18 Å20 Å2
3----4.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.54 Å
Luzzati d res high-2.6
Refinement stepCycle: LAST / Resolution: 2.6→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6907 0 0 387 7294
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 674 10.7 %
Rwork0.337 5622 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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