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- PDB-3vse: Crystal structure of methyltransferase -

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Basic information

Entry
Database: PDB / ID: 3vse
TitleCrystal structure of methyltransferase
ComponentsPutative uncharacterized protein
KeywordsTRANSFERASE / Rossmann fold / METHYLTRANSFERASE
Function / homology
Function and homology information


methyltransferase activity / methylation / RNA binding
Similarity search - Function
RlmI, PUA-like domain / PUA-like domain / RNA methyltransferase domain (HRMD) like / S-adenosylmethionine-dependent methyltransferase / S-adenosylmethionine-dependent methyltransferase / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Transcription Regulator spoIIAA / PUA domain superfamily / PUA domain profile. ...RlmI, PUA-like domain / PUA-like domain / RNA methyltransferase domain (HRMD) like / S-adenosylmethionine-dependent methyltransferase / S-adenosylmethionine-dependent methyltransferase / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Transcription Regulator spoIIAA / PUA domain superfamily / PUA domain profile. / PUA-like superfamily / Vaccinia Virus protein VP39 / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Class I SAM-dependent rRNA methyltransferase / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsKita, S. / Tanaka, Y. / Yao, M. / Tanaka, I.
CitationJournal: Protein Pept.Lett. / Year: 2012
Title: Crystal structure of a putative methyltransferase SAV1081 from Staphylococcus aureus
Authors: Kita, S. / Tanaka, Y. / Hirano, N. / Kimura, S. / Suzuki, T. / Suzuki, T. / Yao, M. / Tanaka, I.
History
DepositionApr 25, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: 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 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)185,0088
Polymers183,4704
Non-polymers1,5384
Water10,449580
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2522
Polymers45,8681
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2522
Polymers45,8681
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2522
Polymers45,8681
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2522
Polymers45,8681
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.485, 91.573, 102.631
Angle α, β, γ (deg.)90.00, 94.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative uncharacterized protein


Mass: 45867.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: SAV1081 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q99V16, UniProt: A0A0H3JYW8*PLUS
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


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


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100mM sodium acetate pH4.5, 40 %(v/v) ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9798 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 22, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. obs: 103003 / % possible obs: 99.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 26.86 Å2
Reflection shellResolution: 2.1→2.14 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: dev_1021)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.099→34.126 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.8392 / SU ML: 0.23 / σ(F): 0 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 5145 5 %
Rwork0.2027 --
obs0.204 102881 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.95 Å2 / Biso mean: 20.9407 Å2 / Biso min: 3.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.922 Å2-0 Å2-2.6003 Å2
2--6.2102 Å2-0 Å2
3----3.7993 Å2
Refinement stepCycle: LAST / Resolution: 2.099→34.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12634 0 104 580 13318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02113066
X-RAY DIFFRACTIONf_angle_d1.44917656
X-RAY DIFFRACTIONf_dihedral_angle_d14.1564778
X-RAY DIFFRACTIONf_chiral_restr0.1261891
X-RAY DIFFRACTIONf_plane_restr0.0062247
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0991-2.1230.26131890.2423200338999
2.123-2.14790.28131690.238532473416100
2.1479-2.17410.29331730.240432423415100
2.1741-2.20160.2771550.225632483403100
2.2016-2.23060.30651650.239132603425100
2.2306-2.26110.33531540.2553195334999
2.2611-2.29340.26451650.22633043469100
2.2934-2.32770.27161720.215732513423100
2.3277-2.3640.22831660.225432423408100
2.364-2.40280.27991830.236132323415100
2.4028-2.44420.3081730.230632403413100
2.4442-2.48860.25291860.217432333419100
2.4886-2.53650.27971690.216632393408100
2.5365-2.58820.24371860.205532603446100
2.5882-2.64450.24061650.214132713436100
2.6445-2.7060.26491740.213532233397100
2.706-2.77360.22851740.219832603434100
2.7736-2.84860.24841900.212432283418100
2.8486-2.93240.23581770.206232623439100
2.9324-3.0270.23341650.212132483413100
3.027-3.13510.26051650.219932893454100
3.1351-3.26050.27371840.207332213405100
3.2605-3.40880.21161670.198433083475100
3.4088-3.58830.20491710.193132393410100
3.5883-3.81280.21860.195932963482100
3.8128-4.10680.21141740.187332523426100
4.1068-4.51920.16981780.166432873465100
4.5192-5.17120.17211590.159933053464100
5.1712-6.50780.23051510.233323483100
6.5078-34.13020.17941600.18183322348298

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