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- PDB-3rfb: Structure of fRMsr -

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Basic information

Entry
Database: PDB / ID: 3rfb
TitleStructure of fRMsr
ComponentsPutative uncharacterized protein
KeywordsOXIDOREDUCTASE / fRMsr / GAF / SME
Function / homology
Function and homology information


L-methionine (R)-S-oxide reductase activity / cytosol
Similarity search - Function
: / GAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
METHIONINE SULFOXIDE / GAF domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBong, S.M. / Chi, Y.M.
CitationJournal: to be published
Title: Structure of fRMsr
Authors: Bong, S.M. / Chi, Y.M.
History
DepositionApr 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8584
Polymers38,5282
Non-polymers3302
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-16 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.242, 101.242, 69.908
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative uncharacterized protein / Free Methionine-R-sulfoxide reductase / fRMsr


Mass: 19263.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: spr0768 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8DQA6, L-methionine (R)-S-oxide reductase
#2: Chemical ChemComp-SME / METHIONINE SULFOXIDE


Type: L-peptide linking / Mass: 165.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 400, Ammonium acetate, sodium citrate tribasic dehydrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23968 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23968 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 18660 / Num. obs: 18660 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.44 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VHM

1vhm


Resolution: 2.3→37.14 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.27 909 RANDOM
Rwork0.23 --
all-18660 -
obs-18639 -
Refinement stepCycle: LAST / Resolution: 2.3→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2527 0 20 80 2627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1.21

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