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- PDB-6aw9: 2.55A resolution structure of SAH bound catechol O-methyltransfer... -

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Basic information

Entry
Database: PDB / ID: 6aw9
Title2.55A resolution structure of SAH bound catechol O-methyltransferase (COMT) L136M 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
S-ADENOSYL-L-HOMOCYSTEINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesNannospalax galili (Upper Galilee mountains blind mole rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 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 ...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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catechol O-methyltransferase
B: Catechol O-methyltransferase
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4809
Polymers77,2063
Non-polymers1,2736
Water61334
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1603
Polymers25,7351
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1603
Polymers25,7351
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1603
Polymers25,7351
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.297, 102.410, 125.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25735.410 Da / Num. of mol.: 3 / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.64 Å3/Da / Density % sol: 53.34 % / Mosaicity: 0.14 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 14.4 % (w/v) PEG 8000, 80 mM sodium cacodylate, 160 mM calcium chloride, 20% glycerol

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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: Apr 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→49.49 Å / Num. obs: 27248 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 52.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Net I/σ(I): 11.7 / Num. measured all: 179065 / Scaling rejects: 0
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.2 / Num. measured all: 21344 / Num. unique all: 3260 / CC1/2: 0.791 / Net I/σ(I) obs: 1.5 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.76 Å47.42 Å
Translation6.76 Å47.42 Å

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Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
PHASER2.6.1phasing
PHENIX(dev_2510: ???)refinement
PDB_EXTRACT3.22data extraction
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLB

2zlb


Resolution: 2.55→44.579 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.72
RfactorNum. reflection% reflection
Rfree0.2588 1370 5.04 %
Rwork0.2075 --
obs0.2103 27176 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.27 Å2 / Biso mean: 70.9638 Å2 / Biso min: 34.25 Å2
Refinement stepCycle: final / Resolution: 2.55→44.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 81 34 4985
Biso mean--62.97 57.86 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025047
X-RAY DIFFRACTIONf_angle_d0.5656872
X-RAY DIFFRACTIONf_chiral_restr0.04796
X-RAY DIFFRACTIONf_plane_restr0.003878
X-RAY DIFFRACTIONf_dihedral_angle_d11.5543046
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.64110.42371390.32652519265899
2.6411-2.74690.41241280.29532554268299
2.7469-2.87190.36281230.28772541266499
2.8719-3.02320.36251240.27782545266999
3.0232-3.21260.29771430.235425482691100
3.2126-3.46060.31181190.215825752694100
3.4606-3.80870.21211390.19662574271399
3.8087-4.35940.2211740.171925712745100
4.3594-5.49080.19921510.16526082759100
5.4908-44.58560.25881300.19812771290199

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