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- PDB-6aw7: 2.15A resolution structure of SAH bound catechol O-methyltransfer... -

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Basic information

Entry
Database: PDB / ID: 6aw7
Title2.15A resolution structure of SAH bound 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
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: 2.15 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2846
Polymers51,4352
Non-polymers8494
Water2,990166
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1423
Polymers25,7171
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1423
Polymers25,7171
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.353, 86.671, 104.116
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 / COMT


Mass: 25717.373 Da / Num. of mol.: 2 / 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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
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: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→45.13 Å / Num. obs: 30921 / % possible obs: 99.9 % / Observed criterion σ(I): 0.115 / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.049 / Net I/σ(I): 12
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2640 / CC1/2: 0.742 / Rsym value: 0.391 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.75 Å45.13 Å
Translation6.75 Å45.13 Å

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Processing

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

2zlb


Resolution: 2.15→33.513 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 20.49
RfactorNum. reflection% reflection
Rfree0.2138 1506 4.88 %
Rwork0.1722 --
obs0.1742 30859 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.24 Å2 / Biso mean: 34.6708 Å2 / Biso min: 17.92 Å2
Refinement stepCycle: final / Resolution: 2.15→33.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 54 166 3517
Biso mean--29.56 39.15 -
Num. residues----425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063417
X-RAY DIFFRACTIONf_angle_d0.8374649
X-RAY DIFFRACTIONf_chiral_restr0.046535
X-RAY DIFFRACTIONf_plane_restr0.006593
X-RAY DIFFRACTIONf_dihedral_angle_d11.5052065
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
2.15-2.21940.24661240.218526482772
2.2194-2.29870.24081400.198526182758
2.2987-2.39070.27151370.197126022739
2.3907-2.49950.25061320.187826412773
2.4995-2.63120.28291350.192826372772
2.6312-2.7960.22471250.178226822807
2.796-3.01180.23271210.174726492770
3.0118-3.31460.2031380.167226652803
3.3146-3.79370.19041610.151926762837
3.7937-4.77740.18741540.139226922846
4.7774-33.51660.20391390.191828432982

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