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- PDB-1vhy: Crystal structure of Haemophilus influenzae protein HI0303, Pfam ... -

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Basic information

Entry
Database: PDB / ID: 1vhy
TitleCrystal structure of Haemophilus influenzae protein HI0303, Pfam DUF558
ComponentsHypothetical protein HI0303
KeywordsStructural genomics / unknown function / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


rRNA (uridine-N3-)-methyltransferase activity / 16S rRNA (uracil1498-N3)-methyltransferase / rRNA base methylation / cytoplasm
Similarity search - Function
Hypothetical PUA domain-like; domain 1 / Ribosomal RNA small subunit methyltransferase E / Ribosomal RNA small subunit methyltransferase E, methyltransferase domain / Ribosomal RNA small subunit methyltransferase E, PUA-like domain / RNA methyltransferase domain / RNA methyltransferase PUA domain / Ribosomal Protein L25; Chain P / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal ...Hypothetical PUA domain-like; domain 1 / Ribosomal RNA small subunit methyltransferase E / Ribosomal RNA small subunit methyltransferase E, methyltransferase domain / Ribosomal RNA small subunit methyltransferase E, PUA-like domain / RNA methyltransferase domain / RNA methyltransferase PUA domain / Ribosomal Protein L25; Chain P / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / PUA-like superfamily / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase E
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met MAD phasing / Resolution: 1.9 Å
AuthorsStructural GenomiX / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
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
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 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 1.4Feb 3, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_conn
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 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
Revision 1.6Oct 16, 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 protein HI0303
B: Hypothetical protein HI0303


Theoretical massNumber of molelcules
Total (without water)58,0072
Polymers58,0072
Non-polymers00
Water6,089338
1
A: Hypothetical protein HI0303


Theoretical massNumber of molelcules
Total (without water)29,0041
Polymers29,0041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein HI0303


Theoretical massNumber of molelcules
Total (without water)29,0041
Polymers29,0041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-14 kcal/mol
Surface area21280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.895, 76.413, 62.107
Angle α, β, γ (deg.)90.00, 108.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical protein HI0303


Mass: 29003.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0303 / Production host: Escherichia coli (E. coli) / References: UniProt: P44627
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
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, 0.9641
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.96411
ReflectionResolution: 1.9→38.07 Å / Num. all: 40406 / Num. obs: 40406 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 4.9 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: Se-Met MAD phasing / Resolution: 1.9→38.07 Å / σ(F): 0
RfactorNum. reflection
Rfree0.3 2026
Rwork0.229 -
obs-40405
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 349.474 Å2 / ksol: 0.974 e/Å3
Displacement parametersBiso mean: 32.001 Å2
Baniso -1Baniso -2Baniso -3
1--1.948 Å20 Å2-1.03 Å2
2--3.242 Å20 Å2
3----1.945 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.9→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 0 338 3981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d2.158
X-RAY DIFFRACTIONp_planar_tor3.955
X-RAY DIFFRACTIONp_chiral_restr0.132
X-RAY DIFFRACTIONp_plane_restr0.014
X-RAY DIFFRACTIONp_mcbond_it1.764
X-RAY DIFFRACTIONp_mcangle_it2.867
X-RAY DIFFRACTIONp_scbond_it2.929
X-RAY DIFFRACTIONp_scangle_it4.205
Software
*PLUS
Version: 4 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.2

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