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- PDB-1ve3: Crystal structure of PH0226 protein from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 1ve3
TitleCrystal structure of PH0226 protein from Pyrococcus horikoshii OT3
Componentshypothetical protein PH0226Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Dimer / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / S-ADENOSYLMETHIONINE / Methyltransf_25 domain-containing protein
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsLokanath, N.K. / Yamamoto, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2017
Title: Crystal structure of SAM-dependent methyltransferase from Pyrococcus horikoshii.
Authors: Pampa, K.J. / Madan Kumar, S. / Hema, M.K. / Kumara, K. / Naveen, S. / Kunishima, N. / Lokanath, N.K.
History
DepositionMar 26, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.4Jan 1, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jan 22, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list ..._pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 PH0226
B: hypothetical protein PH0226
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9224
Polymers54,1252
Non-polymers7972
Water3,207178
1
A: hypothetical protein PH0226
hetero molecules

A: hypothetical protein PH0226
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9224
Polymers54,1252
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+2/31
2
B: hypothetical protein PH0226
hetero molecules

B: hypothetical protein PH0226
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9224
Polymers54,1252
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)58.167, 58.167, 252.463
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein hypothetical protein PH0226 / Hypothesis / Methyl transferase / SAM dependent methyltransferase


Mass: 27062.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O57965
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.6
Details: PEG 4K, Na acetate, pH 4.6, microbatch, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97882, 0.97945, 1.0
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 28, 2004
RadiationMonochromator: Sl111 double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978821
20.979451
311
ReflectionResolution: 2.1→30 Å / Num. all: 29778 / Num. obs: 29753 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.18
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.4 % / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.33 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2075672.21 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1468 4.9 %RANDOM
Rwork0.236 ---
obs0.236 29753 98.8 %-
all-29778 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.9835 Å2 / ksol: 0.329103 e/Å3
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1-4.13 Å22.31 Å20 Å2
2--4.44 Å20 Å2
3----8.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3655 0 54 178 3887
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 258 5.3 %
Rwork0.262 4589 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SAM.PARAMSAM.TOP

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