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- PDB-3cez: Crystal structure of methionine-R-sulfoxide reductase from Burkho... -

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Basic information

Entry
Database: PDB / ID: 3cez
TitleCrystal structure of methionine-R-sulfoxide reductase from Burkholderia pseudomallei
ComponentsMethionine-R-sulfoxide reductase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / BURKHOLDERIA / MSRB / 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
ACETIC ACID / Peptide methionine sulfoxide reductase MsrB
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStaker, B. / Napuli, A. / Nakazawa, S.H. / Castaneda, L. / Alkafeef, S. / Vanvoorhis, W. / Stewart, L. / Myler, P. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Methionine-R-sulfoxide reductase from Burkholderia pseudomallei.
Authors: Staker, B. / Napuli, A. / Nakazawa, S.H. / Castaneda, L. / Alkafeef, S. / Vanvoorhis, W. / Stewart, L. / Myler, P.
History
DepositionFeb 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 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)37,2506
Polymers36,9992
Non-polymers2514
Water4,017223
1
A: Methionine-R-sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6253
Polymers18,5001
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionine-R-sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6253
Polymers18,5001
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.093, 45.782, 45.812
Angle α, β, γ (deg.)87.35, 83.22, 69.36
Int Tables number1
Space group name H-MP1
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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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 (bacteria) / Strain: 1710b / Gene: msrB, BURPS1710b_2458 / Plasmid: AVA0421 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JRF0, EC: 1.8.4.6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15% Ethanol, 100 mM MES pH 6.0, 200 mM Zn(OAc)2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 26, 2008 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→31.42 Å / Num. obs: 17575 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.21
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1583 / % possible all: 85.1

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L1D

1l1d


Resolution: 2.1→31.42 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 4.091 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23367 892 5.1 %RANDOM
Rwork0.17612 ---
obs0.17896 16682 94.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å2-0.92 Å2-0.13 Å2
2--0.39 Å2-0.01 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 10 223 2271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212102
X-RAY DIFFRACTIONr_bond_other_d0.0010.021404
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9432853
X-RAY DIFFRACTIONr_angle_other_deg0.91133392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05523.458107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43915310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8251514
X-RAY DIFFRACTIONr_chiral_restr0.0770.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022410
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02454
X-RAY DIFFRACTIONr_nbd_refined0.1920.2370
X-RAY DIFFRACTIONr_nbd_other0.20.21464
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2984
X-RAY DIFFRACTIONr_nbtor_other0.0820.21029
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2196
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8161.51387
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22522072
X-RAY DIFFRACTIONr_scbond_it1.7633895
X-RAY DIFFRACTIONr_scangle_it2.4684.5781
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.22 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 49
Rwork0.185 1016

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