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- PDB-6aw5: 1.90A resolution structure of catechol O-methyltransferase (COMT)... -

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Basic information

Entry
Database: PDB / ID: 6aw5
Title1.90A resolution structure of catechol O-methyltransferase (COMT) L136M (hexagonal form) from Nannospalax galili
ComponentsCatechol O-methyltransferaseCatechol-O-methyltransferase
KeywordsTRANSFERASE / Spalax / COMT / S-adenosylmethionine binding
Function / homology
Function and homology information


catechol O-methyltransferase activity / : / : / catechol O-methyltransferase / catecholamine metabolic process / methylation / magnesium ion binding / plasma membrane
Similarity search - Function
Catechol O-methyltransferase, eukaryotic / O-methyltransferase / Class I-like SAM-dependent 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
Catechol O-methyltransferase
Similarity search - Component
Biological speciesNannospalax galili (Upper Galilee mountains blind mole rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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)25,9215
Polymers25,7351
Non-polymers1864
Water2,162120
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)95.186, 95.186, 75.172
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-303-

CL

21A-511-

HOH

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Components

#1: Protein Catechol O-methyltransferase / Catechol-O-methyltransferase / COMT


Mass: 25735.410 Da / Num. of mol.: 1 / Fragment: M43-P262 / Mutation: L136M
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: A0A452CSQ2*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.82 Å3/Da / Density % sol: 67.8 % / Mosaicity: 0.09 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% (w/v) PEG 3350, 100 mM sodium citrate/citric acid , 200 mM sodium citrate

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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: 1.9→47.59 Å / Num. obs: 30616 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 35.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.2 / Num. measured all: 316128 / Scaling rejects: 42
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.9-1.949.81.3210.7061100
9.11-47.5910.20.0450.992199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.26 Å47.59 Å
Translation6.26 Å47.59 Å

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Processing

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

2zlb


Resolution: 1.9→36.141 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 18.55
RfactorNum. reflection% reflection
Rfree0.1919 1482 4.85 %
Rwork0.1629 --
obs0.1642 30584 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.41 Å2 / Biso mean: 41.6343 Å2 / Biso min: 24.97 Å2
Refinement stepCycle: final / Resolution: 1.9→36.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 9 120 1770
Biso mean--48.26 49.17 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111679
X-RAY DIFFRACTIONf_angle_d1.0312284
X-RAY DIFFRACTIONf_chiral_restr0.058262
X-RAY DIFFRACTIONf_plane_restr0.007294
X-RAY DIFFRACTIONf_dihedral_angle_d13.4431009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.96130.26671480.232326092757
1.9613-2.03140.23761040.208726622766
2.0314-2.11280.25131420.195426182760
2.1128-2.20890.20061280.184426672795
2.2089-2.32530.18871450.16426252770
2.3253-2.4710.16561280.163526282756
2.471-2.66170.21541460.167626392785
2.6617-2.92950.19471400.173626282768
2.9295-3.35310.17651410.161126492790
3.3531-4.22350.19211320.146226632795
4.2235-36.14720.181280.155527142842

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