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- PDB-4u1q: Crystal structure of S-adenosylmethionine-dependent methyltransfe... -

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Basic information

Entry
Database: PDB / ID: 4u1q
TitleCrystal structure of S-adenosylmethionine-dependent methyltransferase SibL in complex with 3HK and SAH
ComponentsSibL
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


S-adenosyl-L-methionine binding / O-methyltransferase activity / methyltransferase activity
Similarity search - Function
Acetylserotonin O-methyltransferase, dimerisation domain / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Acetylserotonin O-methyltransferase, dimerisation domain / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / 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
Chem-3DJ / S-ADENOSYL-L-HOMOCYSTEINE / SibL
Similarity search - Component
Biological speciesStreptosporangium sibiricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.085 Å
Authorsliu, J.S. / Chen, S.C. / Yang, C.S. / Huang, C.H. / Chen, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science CouncilNSC100-2313-B-241-006 Taiwan
CitationJournal: To Be Published
Title: Crystal structure of S-adenosylmethionine-dependent methyltransferase SibL in complex with 3HK and SAH
Authors: liu, J.S. / Chen, S.C. / Yang, C.S. / Huang, C.H. / Chen, Y.
History
DepositionJul 16, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,13012
Polymers155,6954
Non-polymers2,4348
Water17,925995
1
A: SibL
B: SibL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0656
Polymers77,8482
Non-polymers1,2174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-65 kcal/mol
Surface area24580 Å2
MethodPISA
2
C: SibL
D: SibL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0656
Polymers77,8482
Non-polymers1,2174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-63 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.304, 112.783, 143.139
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
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
#2: Chemical
ChemComp-3DJ / (2S)-2-amino-4-(2-amino-3-hydroxyphenyl)-4-oxobutanoic acid


Mass: 224.213 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2O4
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 995 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 2.0 M Ammonium sulfate 0.1 M TRIS hydrochloride pH 8.5

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.085→30 Å / Num. obs: 89602 / % possible obs: 99.8 % / Redundancy: 7.3 % / Net I/σ(I): 23.2
Reflection shellResolution: 2.085→2.18 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 2.085→29.529 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 2000 2.23 %Random selection
Rwork0.1712 ---
obs0.1722 89509 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.085→29.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10556 0 168 995 11719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811004
X-RAY DIFFRACTIONf_angle_d1.08615032
X-RAY DIFFRACTIONf_dihedral_angle_d14.7173888
X-RAY DIFFRACTIONf_chiral_restr0.0421664
X-RAY DIFFRACTIONf_plane_restr0.0061976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0853-2.13740.26791250.19625502X-RAY DIFFRACTION88
2.1374-2.19520.25141440.19656228X-RAY DIFFRACTION100
2.1952-2.25970.29621420.18716235X-RAY DIFFRACTION100
2.2597-2.33270.23311430.18046269X-RAY DIFFRACTION100
2.3327-2.4160.23331430.18086248X-RAY DIFFRACTION100
2.416-2.51270.21441430.17576288X-RAY DIFFRACTION100
2.5127-2.6270.2481440.17716273X-RAY DIFFRACTION100
2.627-2.76540.23211440.17956296X-RAY DIFFRACTION100
2.7654-2.93850.26051430.18716266X-RAY DIFFRACTION100
2.9385-3.16510.22861440.19466308X-RAY DIFFRACTION100
3.1651-3.48320.25241450.18426317X-RAY DIFFRACTION100
3.4832-3.98620.18291430.15786318X-RAY DIFFRACTION99
3.9862-5.01810.16881460.14226353X-RAY DIFFRACTION99
5.0181-29.53230.18521510.16816608X-RAY DIFFRACTION99

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