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- PDB-6aw4: 1.50A resolution structure of catechol O-methyltransferase (COMT)... -

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Basic information

Entry
Database: PDB / ID: 6aw4
Title1.50A resolution structure of catechol O-methyltransferase (COMT) from Nannospalax galili
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / Spalax / COMT / S-adenosylmethionine binding
Function / homology
Function and homology information


catecholamine catabolic process / catechol O-methyltransferase activity / catechol O-methyltransferase / developmental process / dopamine metabolic process / methylation / axon / dendrite / magnesium ion binding / plasma membrane
Similarity search - Function
Catechol O-methyltransferase, eukaryotic / 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
PHOSPHATE ION / Catechol O-methyltransferase
Similarity search - Component
Biological speciesNannospalax galili (Upper Galilee mountains blind mole rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsLovell, S. / Mehzabeen, N. / Battaile, K.P. / Deng, Y. / Hanzlik, R.P. / Shams, I. / Moskovitz, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: To be published
Title: Crystal structure of the catechol-o-methyl transferase (COMT) enzyme of the subterranean mole rat (Spalax) and the effect of L136M substitution
Authors: Deng, Y. / Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Hanzlik, R.P. / Shams, I. / Moskovitz, J.
History
DepositionSep 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4279
Polymers25,7171
Non-polymers7098
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.755, 94.755, 75.934
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catechol O-methyltransferase / COMT


Mass: 25717.373 Da / Num. of mol.: 1 / Fragment: M43-P262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nannospalax galili (Upper Galilee mountains blind mole rat)
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A452CSQ0*PLUS

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Non-polymers , 5 types, 215 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 3.83 Å3/Da / Density % sol: 67.86 % / Mosaicity: 0.09 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.8 M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→47.38 Å / Num. obs: 62014 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 21.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.431 / Num. measured all: 30834 / Num. unique all: 3066 / CC1/2: 0.663 / Net I/σ(I) obs: 1.9 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.29 Å41.03 Å
Translation6.29 Å41.03 Å

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHASER2.5.7phasing
PHENIX(dev_2510: ???)refinement
PDB_EXTRACT3.22data extraction
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLB

2zlb


Resolution: 1.5→34.458 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 15.88
RfactorNum. reflection% reflection
Rfree0.1695 3055 4.93 %
Rwork0.1536 --
obs0.1544 61970 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.57 Å2 / Biso mean: 26.9413 Å2 / Biso min: 13.73 Å2
Refinement stepCycle: final / Resolution: 1.5→34.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 41 207 1911
Biso mean--38.99 37.87 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091753
X-RAY DIFFRACTIONf_angle_d1.082384
X-RAY DIFFRACTIONf_chiral_restr0.06267
X-RAY DIFFRACTIONf_plane_restr0.007302
X-RAY DIFFRACTIONf_dihedral_angle_d10.8551059
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5001-1.52350.22921050.246126922797
1.5235-1.54850.22951460.22826622808
1.5485-1.57520.24381680.21426542822
1.5752-1.60380.24861460.208426422788
1.6038-1.63470.22771270.203326882815
1.6347-1.6680.18191620.195326342796
1.668-1.70430.22231630.185426442807
1.7043-1.74390.20021530.168626482801
1.7439-1.78760.18161500.166626832833
1.7876-1.83590.18161480.165626402788
1.8359-1.88990.20251080.157827032811
1.8899-1.95090.18831330.149726762809
1.9509-2.02060.18411510.151526752826
2.0206-2.10150.18541320.14626762808
2.1015-2.19710.16191220.141626782800
2.1971-2.3130.14151170.136627052822
2.313-2.45780.13621330.134926852818
2.4578-2.64750.1471170.147327212838
2.6475-2.91380.17781320.153526872819
2.9138-3.33520.16731240.153127142838
3.3352-4.20080.14911450.13926952840
4.2008-34.46670.16661730.155627132886

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