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- PDB-1l1d: Crystal structure of the C-terminal methionine sulfoxide reductas... -

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Basic information

Entry
Database: PDB / ID: 1l1d
TitleCrystal structure of the C-terminal methionine sulfoxide reductase domain (MsrB) of N. gonorrhoeae pilB
Componentspeptide methionine sulfoxide reductase
KeywordsOXIDOREDUCTASE / cacodylate complex / cys-arg-asp catalytic triad / met-R(O) reductase / MsrB
Function / homology
Function and homology information


: / peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein modification process / cellular response to oxidative stress / cytoplasm
Similarity search - Function
: / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Peptide methionine sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / Peptide methionine sulfoxide reductase. / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A ...: / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Peptide methionine sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / Peptide methionine sulfoxide reductase. / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Beta Complex / Thioredoxin-like superfamily / Mainly Beta
Similarity search - Domain/homology
CACODYLATE ION / Peptide methionine sulfoxide reductase MsrA/MsrB
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsLowther, W.T. / Weissbach, H. / Etienne, F. / Brot, N. / Matthews, B.W.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The mirrored methionine sulfoxide reductases of Neisseria gonorrhoeae pilB.
Authors: Lowther, W.T. / Weissbach, H. / Etienne, F. / Brot, N. / Matthews, B.W.
History
DepositionFeb 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: peptide methionine sulfoxide reductase
B: peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4525
Polymers34,0412
Non-polymers4113
Water2,234124
1
A: peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1582
Polymers17,0211
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2953
Polymers17,0211
Non-polymers2742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: peptide methionine sulfoxide reductase
hetero molecules

B: peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5896
Polymers34,0412
Non-polymers5484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1700 Å2
ΔGint-9 kcal/mol
Surface area14850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.354, 68.078, 62.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein peptide methionine sulfoxide reductase


Mass: 17020.541 Da / Num. of mol.: 2 / Fragment: MsrB domain, C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: pilB / Plasmid: pet28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P14930, EC: 1.8.4.13, L-methionine (R)-S-oxide reductase
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Tris, cacodylate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
220 mMTris1droppH8.5
310 %(v/v)glycerol1drop
40.1 Msodium cacodylate1reservoirpH6.5
530 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9792, 0.9793, 0.9611
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Jul 21, 2001
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97931
30.96111
ReflectionResolution: 1.85→27.2 Å / Num. obs: 22584 / % possible obs: 89.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.3
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 4.6 / % possible all: 89
Reflection
*PLUS
Num. measured all: 98562 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 89.1 % / Rmerge(I) obs: 0.245

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.85→27.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE STRUCTURE FACTORS REPRESENT THE OPTIMIZED REFERENCE STRUCTURE FACTORS (FPSHA) AS DETERMINED BY SHARP. THE REFERENCE STRUCTURE FACTOR FOR A GIVEN REFLECTION IS DEFINED AS THE AVERAGE OF ...Details: THE STRUCTURE FACTORS REPRESENT THE OPTIMIZED REFERENCE STRUCTURE FACTORS (FPSHA) AS DETERMINED BY SHARP. THE REFERENCE STRUCTURE FACTOR FOR A GIVEN REFLECTION IS DEFINED AS THE AVERAGE OF THE STRUCTURE FACTORS FROM A THREE-WAVELENGTH MAD DATASET WHERE THE HEAVY-ATOM STRUCTURE FACTOR HAS BEEN SUBTRACTED.
RfactorNum. reflectionSelection details
Rfree0.2369 2164 random
Rwork0.2074 --
all-21836 -
obs-21836 -
Displacement parametersBiso mean: 20.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.236 Å
Refinement stepCycle: LAST / Resolution: 1.85→27.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 15 124 2430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_bond_d0.005
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.207 / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS

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