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- PDB-2dvk: Crystal Structure of Hypothetical protein from Aeropyrum pernix -

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Basic information

Entry
Database: PDB / ID: 2dvk
TitleCrystal Structure of Hypothetical protein from Aeropyrum pernix
ComponentsUPF0130 protein APE0816
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
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsLokanath, N.K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Hypothetical protein from Aeropyrum pernix
Authors: Lokanath, N.K. / Kunishima, N.
History
DepositionJul 31, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0130 protein APE0816


Theoretical massNumber of molelcules
Total (without water)21,0231
Polymers21,0231
Non-polymers00
Water3,603200
1
A: UPF0130 protein APE0816

A: UPF0130 protein APE0816


Theoretical massNumber of molelcules
Total (without water)42,0472
Polymers42,0472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2700 Å2
ΔGint-22 kcal/mol
Surface area15330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.870, 70.232, 91.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

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Components

#1: Protein UPF0130 protein APE0816


Mass: 21023.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): 21-CodonPlus (DE3)-RIL / References: UniProt: Q9YDV3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.5 / Details: HEPES, PEG, pH 7.5, microbatch, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B120.919573, 0.919884, 1.0
Detector
TypeIDDetectorDateDetails
RIGAKU1IMAGE PLATEJul 11, 2006RH coated bend cylindrical mirror
RIGAKU2IMAGE PLATEJul 11, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITEMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9195731
30.9198841
ReflectionResolution: 1.8→40 Å / Num. all: 16342 / Num. obs: 16254 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→39.46 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1603995.15 / 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
Rfree0.249 790 4.9 %RANDOM
Rwork0.234 ---
obs0.234 16254 95.6 %-
all-16342 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5388 Å2 / ksol: 0.352144 e/Å3
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.69 Å20 Å20 Å2
2--1.5 Å20 Å2
3---2.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 0 200 1496
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 123 4.8 %
Rwork0.331 2432 -
obs--92.2 %
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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