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- PDB-3cxk: 1.7 A Crystal structure of methionine-R-sulfoxide reductase from ... -

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Basic information

Entry
Database: PDB / ID: 3cxk
Title1.7 A Crystal structure of methionine-R-sulfoxide reductase from Burkholderia pseudomallei: crystallization in a microfluidic crystal card.
ComponentsMethionine-R-sulfoxide reductase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / BURKHOLDERIA / MSRB / MICROFLUIDIC LABCARD / PSI-2 / PROTEIN STRUCTURE INITIATIVE / ACCELERATED TECHNOLOGIES CENTER FOR GENE TO 3D STRUCTURE / ATCG3D / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 / zinc ion binding
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
ACETATE ION / Peptide methionine sulfoxide reductase MsrB
Similarity search - Component
Biological speciesBurkholderia pseudomallei strain
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsLovell, S. / Gerdts, C. / Staker, B. / Craigen, D. / Stewart, L. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: The plug-based nanovolume Microcapillary Protein Crystallization System (MPCS).
Authors: Gerdts, C.J. / Elliott, M. / Lovell, S. / Mixon, M.B. / Napuli, A.J. / Staker, B.L. / Nollert, P. / Stewart, L.
History
DepositionApr 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,2486
Polymers36,9992
Non-polymers2494
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Methionine-R-sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6243
Polymers18,5001
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Methionine-R-sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6243
Polymers18,5001
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.997, 45.171, 45.402
Angle α, β, γ (deg.)88.410, 83.730, 69.100
Int Tables number1
Space group name H-MP1
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS THE SAME AS ASYMMETRIC UNIT.

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Components

#1: Protein Methionine-R-sulfoxide reductase


Mass: 18499.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei strain / Strain: 1710b / Gene: msrB, BURPS1710b_2458, YP_333853 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q3JRF0, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 293 K / Method: microfluidic microbatch in a crystal card / pH: 4.5
Details: 30% MPD, 0.1M Acetate, 25% PEG 1500, pH 4.5, MICROFLUIDIC MICROBATCH IN A CRYSTAL CARD, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979315 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 11, 2008 / Details: Adjustable focusing mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979315 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 32539 / % possible obs: 95.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.068 / Χ2: 1.116 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.763.30.42330230.562187.4
1.76-1.833.60.29731380.621192.5
1.83-1.913.70.22532740.688195.5
1.91-2.023.80.16432360.731196.2
2.02-2.143.70.12333230.803196.8
2.14-2.313.70.09533030.944196.8
2.31-2.543.70.0833241.099197.5
2.54-2.913.70.06633321.379197.6
2.91-3.663.50.05333251.814197.1
3.66-503.60.05132612.467195.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.93 Å22.15 Å
Translation1.93 Å22.15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.4.0069refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CEZ

3cez


Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.164 / SU B: 1.85 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1650 5.1 %RANDOM
Rwork0.166 ---
obs0.167 32478 95.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.823 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å2-1.35 Å21.06 Å2
2--0 Å2-0.27 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 10 180 2258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212152
X-RAY DIFFRACTIONr_bond_other_d0.0010.021459
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9492925
X-RAY DIFFRACTIONr_angle_other_deg0.93333537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0495268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66623.519108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7315329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7861514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
X-RAY DIFFRACTIONr_mcbond_it1.0121.51320
X-RAY DIFFRACTIONr_mcbond_other0.2791.5532
X-RAY DIFFRACTIONr_mcangle_it1.78122123
X-RAY DIFFRACTIONr_scbond_it2.6843832
X-RAY DIFFRACTIONr_scangle_it4.2984.5798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.7440.2851090.2122071255385.39
1.744-1.7920.2711290.1922100244291.278
1.792-1.8440.232980.1772123236893.792
1.844-1.90.2141020.1822144235395.453
1.9-1.9620.2131030.172043223496.061
1.962-2.0310.244990.1722001218696.066
2.031-2.1080.199940.171920208196.78
2.108-2.1930.1821000.1591836199497.091
2.193-2.2910.151090.1521773193997.06
2.291-2.4020.222830.1611745187897.338
2.402-2.5310.197850.1621626175797.382
2.531-2.6840.252850.171527165597.402
2.684-2.8690.239980.1711441157397.839
2.869-3.0970.215650.1691356145897.462
3.097-3.3910.186600.1591235133597.004
3.391-3.7880.147670.1561138124396.943
3.788-4.3670.175390.139927105191.912
4.367-5.3330.152500.15485091098.901
5.333-7.4750.211440.20565670199.857
7.475-400.224310.17631640086.75

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