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- PDB-1wy7: crystal structure of a putative RNA methyltransferase PH1948 from... -

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Basic information

Entry
Database: PDB / ID: 1wy7
Titlecrystal structure of a putative RNA methyltransferase PH1948 from Pyrococcus horikoshii
Componentshypothetical protein PH1948
KeywordsTRANSFERASE / seven-stranded beta sheet / methyltransferase fold / STRUCTURAL GENOMICS
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / methylation / nucleic acid binding
Similarity search - Function
: / Methyltransferase small domain / Methyltransferase small domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase-like protein 5
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsGao, Y.G. / Yao, M. / Tanaka, I.
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of the putative RNA methyltransferase PH1948 from Pyrococcus horikoshii, in complex with the copurified S-adenosyl-L-homocysteine
Authors: Gao, Y.G. / Yao, M. / Yong, Z. / Tanaka, I.
History
DepositionFeb 8, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: hypothetical protein PH1948
B: hypothetical protein PH1948
C: hypothetical protein PH1948
D: hypothetical protein PH1948
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6598
Polymers95,1214
Non-polymers1,5384
Water5,621312
1
A: hypothetical protein PH1948
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1652
Polymers23,7801
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein PH1948
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1652
Polymers23,7801
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: hypothetical protein PH1948
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1652
Polymers23,7801
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: hypothetical protein PH1948
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1652
Polymers23,7801
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.975, 43.141, 118.240
Angle α, β, γ (deg.)90.00, 92.08, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a monomer.

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Components

#1: Protein
hypothetical protein PH1948


Mass: 23780.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1948 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): B834-DE3
References: UniProt: O59611, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


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.: 312 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 55.629986 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG400, HEPES-Na, CaCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→39.86 Å / Num. all: 53514 / Num. obs: 53514 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 47.46 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 20
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 5.6 / Num. unique all: 5050 / Rsym value: 0.218 / % possible all: 94.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 5222 9.8 %random
Rwork0.242 ---
all-52894 --
obs-52329 98.3 %-
Solvent computationSolvent model: Throughout / Bsol: 54.88 Å2 / ksol: 35.04 e/Å3
Displacement parametersBiso mean: 45.11 Å2
Baniso -1Baniso -2Baniso -3
1--6.873 Å20 Å2-1.417 Å2
2---3.079 Å20 Å2
3---9.952 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.374 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.367 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6407 0 104 312 6823
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_dihedral_angle_d23.53
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.505
X-RAY DIFFRACTIONc_mcangle_it2.141
X-RAY DIFFRACTIONc_scbond_it2.5
X-RAY DIFFRACTIONc_scangle_it3.324
Refine LS restraints NCSNCS model details: ncs restraints for main chain / Weight Biso : 0.3 / Weight position: 200
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection% reflection
Rfree0.33 500 9.5 %
Rwork0.307 4401 -
obs-4901 93 %

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