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- PDB-4mmn: Structural and biochemical analysis of type II free methionine-R-... -

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Basic information

Entry
Database: PDB / ID: 4mmn
TitleStructural and biochemical analysis of type II free methionine-R-sulfoxide reductase from Thermoplasma acidophilum
ComponentsPutative uncharacterized protein Ta0848
KeywordsOXIDOREDUCTASE / reductase
Function / homologyGAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / GAF domain-containing protein
Function and homology information
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKim, H.S. / Kwak, G.H. / Lee, K.T. / Jo, C.H. / Hwang, K.Y. / Kim, H.Y.
CitationJournal: Arch.Biochem.Biophys. / Year: 2014
Title: Structural and biochemical analysis of a type II free methionine-R-sulfoxide reductase from Thermoplasma acidophilum
Authors: Kim, H.S. / Kwak, G.H. / Lee, K. / Jo, C.H. / Hwang, K.Y. / Kim, H.Y.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein Ta0848
B: Putative uncharacterized protein Ta0848
C: Putative uncharacterized protein Ta0848
D: Putative uncharacterized protein Ta0848
E: Putative uncharacterized protein Ta0848
F: Putative uncharacterized protein Ta0848
G: Putative uncharacterized protein Ta0848
H: Putative uncharacterized protein Ta0848


Theoretical massNumber of molelcules
Total (without water)136,1158
Polymers136,1158
Non-polymers00
Water3,189177
1
A: Putative uncharacterized protein Ta0848
B: Putative uncharacterized protein Ta0848


Theoretical massNumber of molelcules
Total (without water)34,0292
Polymers34,0292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Putative uncharacterized protein Ta0848
E: Putative uncharacterized protein Ta0848


Theoretical massNumber of molelcules
Total (without water)34,0292
Polymers34,0292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative uncharacterized protein Ta0848
H: Putative uncharacterized protein Ta0848


Theoretical massNumber of molelcules
Total (without water)34,0292
Polymers34,0292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Putative uncharacterized protein Ta0848
G: Putative uncharacterized protein Ta0848


Theoretical massNumber of molelcules
Total (without water)34,0292
Polymers34,0292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.902, 158.902, 194.596
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Putative uncharacterized protein Ta0848


Mass: 17014.346 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic)
Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
Gene: Ta0848 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HJW5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 3.47 Å3/Da / Density % sol: 64.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.17M ammonium acetate, 0.085M sodium acetate trihydrate (pH 4.6), 25.5% polyethylene glycol 4000, 15% glycerol. , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 54183 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 14.205
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 1.4 / Num. unique all: 265551 / Rsym value: 0.389 / % possible all: 73.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MMH

3mmh


Resolution: 2.6→28.089 Å / SU ML: 0.42 / σ(F): 2.12 / Phase error: 26.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 1991 3.68 %
Rwork0.1956 --
obs0.1971 54100 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→28.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8912 0 0 177 9089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099096
X-RAY DIFFRACTIONf_angle_d1.1912276
X-RAY DIFFRACTIONf_dihedral_angle_d13.623404
X-RAY DIFFRACTIONf_chiral_restr0.0491344
X-RAY DIFFRACTIONf_plane_restr0.0061588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.66530.30771060.3087303977
2.6653-2.73730.37411390.3461352690
2.7373-2.81770.37011290.3245354695
2.8177-2.90860.36221520.3205374396
2.9086-3.01240.35781360.2893372496
3.0124-3.13290.32761480.2648372497
3.1329-3.27530.27541460.2481385198
3.2753-3.44770.2861480.219382399
3.4477-3.66330.23121590.191386899
3.6633-3.94540.20131360.16813790100
3.9454-4.34110.16961600.15123912100
4.3411-4.96630.17041480.12643868100
4.9663-6.24570.20391360.15143892100
6.2457-28.09090.20781480.155380398

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