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- PDB-2drv: Structure of PH1069 protein from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2drv
TitleStructure of PH1069 protein from Pyrococcus horikoshii OT3
ComponentsUPF0130 protein PH1069
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


tRNAPhe 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine37-N4]-methyltransferase / wybutosine biosynthetic process / tRNA methyltransferase activity / tRNA methylation
Similarity search - Function
SSo0622-like fold / tRNA wybutosine-synthesizing-like / tRNA wybutosine-synthesizing protein / tRNA(Phe) 7-((3-amino-3-carboxypropyl)-4-demethylwyosine(37)-N(4))-methyltransferase / tRNA wybutosine-synthesizing-like superfamily / Methyltransferase TYW3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA(Phe) 7-((3-amino-3-carboxypropyl)-4-demethylwyosine(37)-N(4))-methyltransferase 1
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsLokanath, N.K. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of PH1069 protein from Pyrococcus horikoshii OT3
Authors: Lokanath, N.K. / Kunishima, N.
History
DepositionJun 15, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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: UPF0130 protein PH1069
B: UPF0130 protein PH1069
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1853
Polymers47,0892
Non-polymers961
Water6,828379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.346, 52.898, 53.125
Angle α, β, γ (deg.)104.65, 102.96, 109.25
Int Tables number1
Space group name H-MP1

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Components

#1: Protein UPF0130 protein PH1069


Mass: 23544.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3)-RIL / References: UniProt: O58796
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.2 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.6
Details: Sodium acetate, Ammonium sulfate, 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: 0.979141, 0.97341, 1.0
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 16, 2006
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791411
20.973411
311
ReflectionResolution: 1.6→40 Å / Num. all: 43824 / Num. obs: 43824 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.7
Reflection shellResolution: 1.6→1.66 Å / % possible all: 90.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→36.82 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 731548.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2192 5 %RANDOM
Rwork0.218 ---
obs0.218 43824 95.4 %-
all-43824 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.2634 Å2 / ksol: 0.430583 e/Å3
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.59 Å21.33 Å2-1.83 Å2
2---1.53 Å2-1.07 Å2
3----2.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.6→36.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 5 379 3548
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 350 5.4 %
Rwork0.285 6158 -
obs--84.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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