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- PDB-3tfw: Crystal structure of a putative O-methyltransferase from Klebsiel... -

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Basic information

Entry
Database: PDB / ID: 3tfw
TitleCrystal structure of a putative O-methyltransferase from Klebsiella pneumoniae
ComponentsPutative O-methyltransferase
KeywordsTRANSFERASE / PSI-Biology / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation
Similarity search - Function
: / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsSatyanarayana, L. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a putative O-methyltransferase from Klebsiella pneumoniae
Authors: Satyanarayana, L. / Almo, S.C. / Swaminathan, S.
History
DepositionAug 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative O-methyltransferase
B: Putative O-methyltransferase


Theoretical massNumber of molelcules
Total (without water)56,1922
Polymers56,1922
Non-polymers00
Water4,720262
1
A: Putative O-methyltransferase

B: Putative O-methyltransferase


Theoretical massNumber of molelcules
Total (without water)56,1922
Polymers56,1922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area4400 Å2
ΔGint-41 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.285, 95.305, 56.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative O-methyltransferase


Mass: 28095.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Top 10 cells (Invitrogen)
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: KPN78578_14560, KPN_01485 / Plasmid details: T7 promoter / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon + RIL / References: UniProt: A6T8J6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.04 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.2% w/v n-Octyl-b-D-glucoside, 0.2M Ammonium Sulphate and 30% w/v Polyethylene glycol 8,000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2010 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 38046 / Num. obs: 38046 / % possible obs: 99.5 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.53 / Num. unique all: 3587 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELX& Arp/Warpmodel building
REFMAC5.5.0109refinement
DENZOdata reduction
HKL-2000data scaling
SHELX& Arp/Warpphasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.291 / SU ML: 0.1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1861 4.9 %RANDOM
Rwork0.20404 ---
obs0.20602 36043 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.773 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20 Å2
2--1.63 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 0 262 3687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223495
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9514761
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7595439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02124.186172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07515562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0741530
X-RAY DIFFRACTIONr_chiral_restr0.0730.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212708
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6251.52189
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21323503
X-RAY DIFFRACTIONr_scbond_it1.99231306
X-RAY DIFFRACTIONr_scangle_it3.3184.51258
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.928 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 114 -
Rwork0.246 2578 -
obs--98.25 %

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