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- PDB-1to0: X-ray structure of Northeast Structural Genomics target protein s... -

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Basic information

Entry
Database: PDB / ID: 1to0
TitleX-ray structure of Northeast Structural Genomics target protein sr145 from Bacillus subtilis
ComponentsHypothetical UPF0247 protein yyda
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


23S rRNA (pseudouridine1915-N3)-methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase activity / cytoplasm
Similarity search - Function
RNA methyltransferase RlmH / Predicted SPOUT methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA large subunit methyltransferase H
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKuzin, A.P. / Edstrom, W. / Vorobiev, S.M. / Shastry, R. / Ma, L.-C. / Xiao, R. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-ray structure of Northeast Structural Genomics target protein sr145 from Bacillus subtilis
Authors: Kuzin, A.P. / Edstrom, W. / Vorobiev, S.M. / Shastry, R. / Ma, L.-C. / Xiao, R. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJun 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical UPF0247 protein yyda
B: Hypothetical UPF0247 protein yyda
C: Hypothetical UPF0247 protein yyda
D: Hypothetical UPF0247 protein yyda
E: Hypothetical UPF0247 protein yyda
F: Hypothetical UPF0247 protein yyda
G: Hypothetical UPF0247 protein yyda
H: Hypothetical UPF0247 protein yyda


Theoretical massNumber of molelcules
Total (without water)155,6458
Polymers155,6458
Non-polymers00
Water3,279182
1
A: Hypothetical UPF0247 protein yyda
B: Hypothetical UPF0247 protein yyda


Theoretical massNumber of molelcules
Total (without water)38,9112
Polymers38,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-19 kcal/mol
Surface area14380 Å2
MethodPISA
2
C: Hypothetical UPF0247 protein yyda
D: Hypothetical UPF0247 protein yyda


Theoretical massNumber of molelcules
Total (without water)38,9112
Polymers38,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-19 kcal/mol
Surface area15230 Å2
MethodPISA
3
E: Hypothetical UPF0247 protein yyda
F: Hypothetical UPF0247 protein yyda


Theoretical massNumber of molelcules
Total (without water)38,9112
Polymers38,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-19 kcal/mol
Surface area13730 Å2
MethodPISA
4
G: Hypothetical UPF0247 protein yyda
H: Hypothetical UPF0247 protein yyda


Theoretical massNumber of molelcules
Total (without water)38,9112
Polymers38,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-19 kcal/mol
Surface area14610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.691, 70.553, 100.488
Angle α, β, γ (deg.)90.00, 95.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypothetical UPF0247 protein yyda


Mass: 19455.645 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YYDA, BSU40230 / Plasmid: pet21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q45601
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18-20 % PEG 3350, 0.2 M KCl, 50 mM TrisHCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 113561 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.89 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.516 / % possible all: 77

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VH0

1vh0


Resolution: 2.5→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 364813.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.29 3897 4.9 %RANDOM
Rwork0.237 ---
obs0.237 78887 84.6 %-
all-87680 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.3779 Å2 / ksol: 0.271662 e/Å3
Displacement parametersBiso mean: 44.2 Å2
Baniso -1Baniso -2Baniso -3
1--9.45 Å20 Å23.79 Å2
2--13.35 Å20 Å2
3----3.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9353 0 0 182 9535
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.7671.5
X-RAY DIFFRACTIONc_mcangle_it3.1292
X-RAY DIFFRACTIONc_scbond_it2.6022
X-RAY DIFFRACTIONc_scangle_it3.9312.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 526 5.4 %
Rwork0.275 9304 -
obs--63.3 %
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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