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- PDB-4qvg: Crystal structure of S-adenosylmethionine-dependent methyltransfe... -

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Basic information

Entry
Database: PDB / ID: 4qvg
TitleCrystal structure of S-adenosylmethionine-dependent methyltransferase SibL in its apo form
ComponentsSibL
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


S-adenosyl-L-methionine binding / O-methyltransferase activity / methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
: / Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...: / Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptosporangium sibiricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLiu, J.S. / Chen, S.C. / Huang, C.H. / Yang, C.S. / Chen, Y.
CitationJournal: Sci Rep / Year: 2015
Title: Structure and mechanism of an antibiotics-synthesizing 3-hydroxykynurenine C-methyltransferase
Authors: Chen, S.C. / Huang, C.H. / Lai, S.J. / Liu, J.S. / Fu, P.K. / Tseng, S.T. / Yang, C.S. / Lai, M.C. / Ko, T.P. / Chen, Y.
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 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: SibL
B: SibL
C: SibL
D: SibL


Theoretical massNumber of molelcules
Total (without water)155,6954
Polymers155,6954
Non-polymers00
Water00
1
A: SibL

A: SibL


Theoretical massNumber of molelcules
Total (without water)77,8482
Polymers77,8482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7000 Å2
ΔGint-61 kcal/mol
Surface area28010 Å2
MethodPISA
2
B: SibL
C: SibL


Theoretical massNumber of molelcules
Total (without water)77,8482
Polymers77,8482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-66 kcal/mol
Surface area28330 Å2
MethodPISA
3
D: SibL

D: SibL


Theoretical massNumber of molelcules
Total (without water)77,8482
Polymers77,8482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y+1/2,-z-1/21
Buried area7030 Å2
ΔGint-60 kcal/mol
Surface area28060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.931, 295.421, 322.231
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein
SibL


Mass: 38923.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptosporangium sibiricum (bacteria) / Gene: sibL / Production host: Escherichia coli (E. coli) / References: UniProt: C0LTM6

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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: 3.93 Å3/Da / Density % sol: 68.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 10%(v/v) Polyethylene glycol 200, 0.1 M BIS-TRIS propane pH 9.0, 18%(w/v) Polyethylene glycol 8,000 , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 54894 / Num. obs: 54730 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.211 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U1Q

4u1q


Resolution: 2.9→28.116 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2658 2001 3.66 %RANDOM
Rwork0.2115 ---
obs0.2135 54665 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→28.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10596 0 0 0 10596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110871
X-RAY DIFFRACTIONf_angle_d1.38214845
X-RAY DIFFRACTIONf_dihedral_angle_d12.6393871
X-RAY DIFFRACTIONf_chiral_restr0.0781647
X-RAY DIFFRACTIONf_plane_restr0.0091964
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 (%)
2.8871-2.95920.3531310.2919350594
2.9592-3.03910.35691540.28593738100
3.0391-3.12840.41721320.27573798100
3.1284-3.22930.28461380.25823728100
3.2293-3.34450.36181500.25883744100
3.3445-3.47820.27541380.2513771100
3.4782-3.63620.28371560.23373746100
3.6362-3.82740.26771280.21433805100
3.8274-4.06660.25541430.20423751100
4.0666-4.37950.24181500.19883774100
4.3795-4.81820.26061450.189377899
4.8182-5.51090.2291430.1973794100
5.5109-6.92590.25341440.21583854100
6.9259-28.11780.22591490.1654387898

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