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- PDB-1vh0: Crystal structure of a hypothetical protein -

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Basic information

Entry
Database: PDB / ID: 1vh0
TitleCrystal structure of a hypothetical protein
ComponentsHypothetical UPF0247 protein SAV0024/SA0023
KeywordsStructural genomics / unknown function
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 / Ribosomal RNA large subunit methyltransferase H
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionNov 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical UPF0247 protein SAV0024/SA0023
B: Hypothetical UPF0247 protein SAV0024/SA0023
C: Hypothetical UPF0247 protein SAV0024/SA0023
D: Hypothetical UPF0247 protein SAV0024/SA0023
E: Hypothetical UPF0247 protein SAV0024/SA0023
F: Hypothetical UPF0247 protein SAV0024/SA0023


Theoretical massNumber of molelcules
Total (without water)111,2086
Polymers111,2086
Non-polymers00
Water5,783321
1
A: Hypothetical UPF0247 protein SAV0024/SA0023


Theoretical massNumber of molelcules
Total (without water)18,5351
Polymers18,5351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical UPF0247 protein SAV0024/SA0023


Theoretical massNumber of molelcules
Total (without water)18,5351
Polymers18,5351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical UPF0247 protein SAV0024/SA0023


Theoretical massNumber of molelcules
Total (without water)18,5351
Polymers18,5351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hypothetical UPF0247 protein SAV0024/SA0023


Theoretical massNumber of molelcules
Total (without water)18,5351
Polymers18,5351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Hypothetical UPF0247 protein SAV0024/SA0023


Theoretical massNumber of molelcules
Total (without water)18,5351
Polymers18,5351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Hypothetical UPF0247 protein SAV0024/SA0023


Theoretical massNumber of molelcules
Total (without water)18,5351
Polymers18,5351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
E: Hypothetical UPF0247 protein SAV0024/SA0023
F: Hypothetical UPF0247 protein SAV0024/SA0023


Theoretical massNumber of molelcules
Total (without water)37,0692
Polymers37,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-21 kcal/mol
Surface area15410 Å2
MethodPISA, PQS
8
A: Hypothetical UPF0247 protein SAV0024/SA0023
B: Hypothetical UPF0247 protein SAV0024/SA0023


Theoretical massNumber of molelcules
Total (without water)37,0692
Polymers37,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-19 kcal/mol
Surface area15180 Å2
MethodPISA, PQS
9
C: Hypothetical UPF0247 protein SAV0024/SA0023
D: Hypothetical UPF0247 protein SAV0024/SA0023


Theoretical massNumber of molelcules
Total (without water)37,0692
Polymers37,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-19 kcal/mol
Surface area15140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.527, 74.496, 81.531
Angle α, β, γ (deg.)91.06, 107.14, 90.14
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Hypothetical UPF0247 protein SAV0024/SA0023


Mass: 18534.611 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SAV0024, SA0023 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0N8, UniProt: P0C1V0*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.86→37.24 Å / Num. all: 87017 / Num. obs: 87017 / % possible obs: 95.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 10.1
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 1.7 / % possible all: 81.8
Reflection shell
*PLUS
% possible obs: 81.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→19.92 Å / σ(F): 0
RfactorNum. reflection
Rfree0.318 2359
Rwork0.26 -
obs-46731
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 67.804 Å2 / ksol: 0.784 e/Å3
Displacement parametersBiso mean: 48.451 Å2
Baniso -1Baniso -2Baniso -3
1-2.525 Å20.226 Å2-0.221 Å2
2---1.647 Å20.752 Å2
3----0.98 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2.31→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7437 0 0 321 7758
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d2.581
X-RAY DIFFRACTIONp_planar_tor2.994
X-RAY DIFFRACTIONp_chiral_restr0.191
X-RAY DIFFRACTIONp_plane_restr0.019
X-RAY DIFFRACTIONp_mcbond_it2.363
X-RAY DIFFRACTIONp_mcangle_it3.742
X-RAY DIFFRACTIONp_scbond_it4.018
X-RAY DIFFRACTIONp_scangle_it5.576
Refinement
*PLUS
Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.6

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