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- PDB-6qa0: MSRB3 - AA 1-137 -

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Basic information

Entry
Database: PDB / ID: 6qa0
TitleMSRB3 - AA 1-137
ComponentsMethionine-R-sulfoxide reductase B3
KeywordsOXIDOREDUCTASE / Enzyme / Methionine Sulfoxide
Function / homology
Function and homology information


L-methionine (R)-S-oxide reductase / L-methionine-(R)-S-oxide reductase activity / peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / Protein repair / protein repair / response to oxidative stress / endoplasmic reticulum / mitochondrion / zinc ion binding ...L-methionine (R)-S-oxide reductase / L-methionine-(R)-S-oxide reductase activity / peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / Protein repair / protein repair / response to oxidative stress / endoplasmic reticulum / mitochondrion / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Peptide methionine sulfoxide reductase MsrB / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Mss4-like superfamily
Similarity search - Domain/homology
Methionine-R-sulfoxide reductase B3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.709 Å
AuthorsJavitt, G. / Fass, D.
CitationJournal: Antioxid.Redox Signal. / Year: 2020
Title: Structure and Electron-Transfer Pathway of the Human Methionine Sulfoxide Reductase MsrB3.
Authors: Javitt, G. / Cao, Z. / Resnick, E. / Gabizon, R. / Bulleid, N.J. / Fass, D.
History
DepositionDec 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 9, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Methionine-R-sulfoxide reductase B3
B: Methionine-R-sulfoxide reductase B3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1066
Polymers31,8432
Non-polymers2624
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-43 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.149, 85.713, 49.167
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Methionine-R-sulfoxide reductase B3 / MsrB3


Mass: 15921.589 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSRB3, UNQ1965/PRO4487 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
References: UniProt: Q8IXL7, peptide-methionine (R)-S-oxide reductase, L-methionine (R)-S-oxide reductase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200mM NaCl, 100mM Sodium Cacodylate pH 7.4, 1.6M Ammonium Sulfate, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Nov 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.71→42.86 Å / Num. obs: 37570 / % possible obs: 99.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 24.88 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.084 / Net I/σ(I): 11.3 / Num. measured all: 159023
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.71-1.744.41.4773217670.6741.40794.5
4.64-42.874.130.3845820710.0180.037100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
xia2data scaling
PDB_EXTRACT3.24data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CEZ

3cez


Resolution: 1.709→42.649 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 1834 4.9 %
Rwork0.1739 35624 -
obs0.1761 37458 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.1 Å2 / Biso mean: 30.8458 Å2 / Biso min: 14.6 Å2
Refinement stepCycle: final / Resolution: 1.709→42.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 8 334 2540
Biso mean--30.26 40.59 -
Num. residues----282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7094-1.75560.32661260.29312585271194
1.7556-1.80720.26641320.261127192851100
1.8072-1.86560.26191450.23722704284999
1.8656-1.93230.28381240.22742717284199
1.9323-2.00960.26961390.21122712285199
2.0096-2.10110.28491570.19912720287799
2.1011-2.21180.20721500.18192711286199
2.2118-2.35040.21871550.17762728288399
2.3504-2.53190.23721490.18152700284998
2.5319-2.78660.21541530.177727792932100
2.7866-3.18970.23741440.172927892933100
3.1897-4.01830.2031300.14492816294699
4.0183-42.6620.181300.14922944307498

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