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- PDB-3mao: Crystal Structure of Human Methionine-R-Sulfoxide Reductase B1 (MsrB1) -

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Basic information

Entry
Database: PDB / ID: 3mao
TitleCrystal Structure of Human Methionine-R-Sulfoxide Reductase B1 (MsrB1)
ComponentsMethionine-R-sulfoxide reductase B1
KeywordsOXIDOREDUCTASE / Structural Genomics Consortium / SGC / Cytoplasm / Metal-binding / Nucleus / Selenocysteine / Zinc
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 / actin filament polymerization / actin cytoskeleton / actin 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 / actin filament polymerization / actin cytoskeleton / actin binding / innate immune response / zinc ion binding / nucleus / cytosol
Similarity search - Function
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
: / MALONATE ION / Methionine-R-sulfoxide reductase B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsChaikuad, A. / Shafqat, N. / Yue, W.W. / Savitsky, P. / Krojer, T. / Ugochukwu, E. / Muniz, J.R.C. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. ...Chaikuad, A. / Shafqat, N. / Yue, W.W. / Savitsky, P. / Krojer, T. / Ugochukwu, E. / Muniz, J.R.C. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Methionine-R-Sulfoxide Reductase B1 (MsrB1)
Authors: Chaikuad, A. / Shafqat, N. / Yue, W.W. / Savitsky, P. / Krojer, T. / Ugochukwu, E. / Muniz, J.R.C. / Pike, A.C.W. / von Delft, F. / H Arrowsmith, C. / Edwards, A.M. / Weigelt, J. / Bountra, ...Authors: Chaikuad, A. / Shafqat, N. / Yue, W.W. / Savitsky, P. / Krojer, T. / Ugochukwu, E. / Muniz, J.R.C. / Pike, A.C.W. / von Delft, F. / H Arrowsmith, C. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium (SGC)
History
DepositionMar 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine-R-sulfoxide reductase B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8666
Polymers11,5601
Non-polymers3065
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.054, 47.473, 57.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methionine-R-sulfoxide reductase B1 / MsrB1 / Selenoprotein X / SelX


Mass: 11559.970 Da / Num. of mol.: 1 / Fragment: Methionine-R-sulfoxide reductase B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPC270, MSRB1, SEPX1, SEPX1 (MsrB1) / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2
References: UniProt: Q9NZV6, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.6M Na Malonate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2010 / Details: two K-B pairs of bimorph type mirrors
RadiationMonochromator: ACCEL Fixed exit Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.42→36.69 Å / Num. all: 18242 / Num. obs: 18197 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.4
Reflection shellResolution: 1.42→1.5 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2552 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3e0o

3e0o


Resolution: 1.42→36.69 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.601 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16964 928 5.1 %RANDOM
Rwork0.1404 ---
all0.14188 18197 --
obs0.14188 17271 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.943 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.42→36.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms844 0 24 143 1011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021893
X-RAY DIFFRACTIONr_bond_other_d0.0030.02639
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.961208
X-RAY DIFFRACTIONr_angle_other_deg0.86631559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4435117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36423.07739
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.33115149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.991155
X-RAY DIFFRACTIONr_chiral_restr0.0990.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211021
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02191
X-RAY DIFFRACTIONr_mcbond_it1.9263543
X-RAY DIFFRACTIONr_mcbond_other0.5433218
X-RAY DIFFRACTIONr_mcangle_it3.0675877
X-RAY DIFFRACTIONr_scbond_it4.3238350
X-RAY DIFFRACTIONr_scangle_it6.28411324
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 56 -
Rwork0.249 1219 -
obs--97.25 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.79110.31190.05780.73250.22020.6577-0.01680.05240-0.00120.0208-0.00640-0.0084-0.0040.01350.0027-0.00210.02080.00240.0284-3.4360.51338.155
241.4659-20.54091.806410.72781.20238.04140.90950.4867-0.0293-0.2822-0.0716-0.19540.72520.7608-0.83790.11450.0867-0.03540.1241-0.02540.17611.7459.47350.493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 105
2X-RAY DIFFRACTION2A106 - 112

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