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- PDB-6q9v: MSRB3 -

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Basic information

Entry
Database: PDB / ID: 6q9v
TitleMSRB3
Components(Methionine-R-sulfoxide reductase ...) x 2
KeywordsOXIDOREDUCTASE / methionine sulfoxide / enzyme / msr
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 / cytoplasm / cytosol
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 / molecular replacement / Resolution: 1.85 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 / struct_conn
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
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)35,53910
Polymers34,7652
Non-polymers7748
Water5,459303
1
A: Methionine-R-sulfoxide reductase B3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9965
Polymers17,5981
Non-polymers3984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionine-R-sulfoxide reductase B3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5435
Polymers17,1671
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.025, 65.183, 112.777
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Methionine-R-sulfoxide reductase ... , 2 types, 2 molecules AB

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


Mass: 17598.439 Da / Num. of mol.: 1
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: Protein Methionine-R-sulfoxide reductase B3 / MsrB3


Mass: 17166.979 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 311 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200mM NaCl, 100mM Cacodylate pH 7.4, 1.6M Ammonium Sulfate, 10% 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.85→56.435 Å / Num. obs: 28505 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.41 Å2 / Rpim(I) all: 0.105 / Rrim(I) all: 0.275 / Net I/σ(I): 4.9 / Num. measured all: 192229
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.85-1.8871.4974913850.6031.6297.9
5.02-56.4356.49.61016615840.0470.1299.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QA0

6qa0


Resolution: 1.85→56.435 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 1463 5.15 %
Rwork0.1819 26948 -
obs0.1842 28411 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.22 Å2 / Biso mean: 23.0244 Å2 / Biso min: 8.6 Å2
Refinement stepCycle: final / Resolution: 1.85→56.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 83 303 2628
Biso mean--35.29 31.4 -
Num. residues----287
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8498-1.91590.30621590.24512651281099
1.9159-1.99260.26621470.221326212768100
1.9926-2.08330.28071520.216726312783100
2.0833-2.19320.22631200.185926932813100
2.1932-2.33060.23281420.186426892831100
2.3306-2.51050.23471530.186326552808100
2.5105-2.76320.25051290.186827042833100
2.7632-3.1630.21361450.18072689283499
3.163-3.98480.20221550.15127412896100
3.9848-56.46080.19841610.173828743035100

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