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- PDB-4z2y: Crystal structure of methyltransferase CalO6 -

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Basic information

Entry
Database: PDB / ID: 4z2y
TitleCrystal structure of methyltransferase CalO6
ComponentsCalO6
KeywordsTRANSFERASE / O-methyltransferase / calicheamicin / anticancer / antibiotic
Function / homology
Function and homology information


O-methyltransferase activity
Similarity search - Function
Acetylserotonin O-methyltransferase, dimerisation domain / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Acetylserotonin O-methyltransferase, dimerisation domain / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsHou, C. / Garneau-Tsodikova, S. / Tsodikov, O.V.
CitationJournal: Bmc Struct.Biol. / Year: 2015
Title: Crystal structure of O-methyltransferase CalO6 from the calicheamicin biosynthetic pathway: a case of challenging structure determination at low resolution.
Authors: Tsodikov, O.V. / Hou, C. / Walsh, C.T. / Garneau-Tsodikova, S.
History
DepositionMar 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CalO6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7143
Polymers38,3121
Non-polymers4012
Water724
1
A: CalO6
hetero molecules

A: CalO6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4276
Polymers76,6252
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6190 Å2
ΔGint-44 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.828, 126.828, 105.659
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein CalO6


Mass: 38312.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calO6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8KND2
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Reservoir: 0.1 M NaCl, 0.1 M Bis-Tris (pH 5.8), and 1.10-1.25 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.007 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 11759 / % possible obs: 98.07 % / Redundancy: 3.4 % / Net I/σ(I): 28

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.4→25 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.846 / SU B: 144.519 / SU ML: 1.032 / Cross valid method: THROUGHOUT / ESU R Free: 0.826 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33338 204 4.5 %RANDOM
Rwork0.32458 ---
obs0.32502 4328 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 110.344 Å2
Baniso -1Baniso -2Baniso -3
1-4.57 Å22.29 Å20 Å2
2--4.57 Å20 Å2
3----14.83 Å2
Refinement stepCycle: 1 / Resolution: 3.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 2 4 2194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192223
X-RAY DIFFRACTIONr_bond_other_d0.0020.022134
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9763030
X-RAY DIFFRACTIONr_angle_other_deg1.05734864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5345297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93322.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.06715330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3731524
X-RAY DIFFRACTIONr_chiral_restr0.0790.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212556
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02492
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_it1.2936.7691194
X-RAY DIFFRACTIONr_mcbond_other1.2736.7681193
X-RAY DIFFRACTIONr_mcangle_it2.3410.1521489
X-RAY DIFFRACTIONr_mcangle_other2.34210.1521490
X-RAY DIFFRACTIONr_scbond_it0.8746.8221029
X-RAY DIFFRACTIONr_scbond_other0.8746.8231030
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.71410.1941542
X-RAY DIFFRACTIONr_long_range_B_refined4.93353.8552523
X-RAY DIFFRACTIONr_long_range_B_other4.93353.8632524
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.404→3.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 16 -
Rwork0.496 313 -
obs--99.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.9693-1.4425-1.79922.1006-2.77616.44150.06120.3146-0.28460.499-0.00530.1743-1.0039-0.1683-0.05580.4131-0.0525-0.03450.0573-0.10060.533117.968757.9089-4.9445
214.8188-2.11915.89210.8622-1.85694.3253-0.76580.25010.76690.0740.2103-0.1999-0.4083-0.30190.55550.3781-0.1039-0.02050.1632-0.08020.319327.382261.00098.7709
35.8756-3.1441-2.57534.31853.93533.63480.13350.16410.3974-0.46630.5265-0.554-0.49620.5903-0.660.3521-0.12740.1210.3677-0.05870.726931.435257.350638.1109
43.17090.042-3.91543.4895-0.65864.9956-0.0929-0.1193-0.2866-0.2685-0.19780.2406-0.03450.17450.29070.3604-0.0923-0.03340.3999-0.04880.588536.399146.265223.456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 92
2X-RAY DIFFRACTION2A93 - 124
3X-RAY DIFFRACTION3A162 - 279
4X-RAY DIFFRACTION4A280 - 345

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