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- PDB-2ift: Crystal structure of putative methylase HI0767 from Haemophilus i... -

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Basic information

Entry
Database: PDB / ID: 2ift
TitleCrystal structure of putative methylase HI0767 from Haemophilus influenzae. NESG target IR102.
ComponentsPutative methylase HI0767
KeywordsTRANSFERASE / NESG / Methylase / Y767_HAEIN / HI0767 / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


16S rRNA (guanine966-N2)-methyltransferase / 16S rRNA (guanine(966)-N(2))-methyltransferase activity / nucleic acid binding
Similarity search - Function
Conserved hypothetical protein 95 / RNA methyltransferase, RsmD / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase D
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVorobiev, S.M. / Su, M. / Seetharaman, J. / Shastry, R. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Acton, T.B. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Shastry, R. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the putative methylase HI0767 from Haemophilus influenzae.
Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Shastry, R. / Janjua, H. / Ma, L.C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative methylase HI0767
B: Putative methylase HI0767


Theoretical massNumber of molelcules
Total (without water)46,3862
Polymers46,3862
Non-polymers00
Water1,928107
1
A: Putative methylase HI0767


Theoretical massNumber of molelcules
Total (without water)23,1931
Polymers23,1931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative methylase HI0767


Theoretical massNumber of molelcules
Total (without water)23,1931
Polymers23,1931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.337, 57.873, 47.522
Angle α, β, γ (deg.)90.00, 107.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative methylase HI0767


Mass: 23193.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0767 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic
References: UniProt: P44869, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 7.5
Details: 19-21% PEG 4000, 0.2 M Ammonium acetate, 0.1 M HEPES, pH 7.5, microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97928 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.3→36.96 Å / Num. all: 64570 / Num. obs: 64570 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.88
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.4 / % possible all: 85.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FPO, Chain F

2fpo


Resolution: 2.3→29.34 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 528428.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: THE FRIEDEL PAIRS WERE USED IN STRUCTURE SOLUTION AND REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1171 4 %RANDOM
Rwork0.223 ---
obs0.223 29138 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.4013 Å2 / ksol: 0.329323 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.7 Å20 Å2-0.29 Å2
2---4.56 Å20 Å2
3---10.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 0 107 2676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 175 4.5 %
Rwork0.258 3731 -
obs--72.3 %
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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