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- PDB-5lsa: human catechol O-methyltransferase in complex with SAM and DNC at... -

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Basic information

Entry
Database: PDB / ID: 5lsa
Titlehuman catechol O-methyltransferase in complex with SAM and DNC at 1.50A
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION
Function / homology
Function and homology information


Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / catecholamine catabolic process / catechol O-methyltransferase activity / catechol O-methyltransferase / developmental process / Methylation / dopamine catabolic process / O-methyltransferase activity / dopamine metabolic process ...Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / catecholamine catabolic process / catechol O-methyltransferase activity / catechol O-methyltransferase / developmental process / Methylation / dopamine catabolic process / O-methyltransferase activity / dopamine metabolic process / methyltransferase activity / lipid metabolic process / methylation / Potential therapeutics for SARS / axon / dendrite / magnesium ion binding / endoplasmic reticulum / extracellular exosome / membrane / plasma membrane / cytosol
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
3,5-DINITROCATECHOL / S-ADENOSYLMETHIONINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsEhler, A. / Lerner, C. / Rudolph, M.G.
CitationJournal: To Be Published
Title: human catechol O-methyltransferase in complex with SAM and DNC at 1.50A
Authors: Lerner, C. / Rudolph, M.G.
History
DepositionAug 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1365
Polymers24,4781
Non-polymers6584
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-20 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.021, 61.311, 44.773
Angle α, β, γ (deg.)90.000, 118.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catechol O-methyltransferase


Mass: 24478.076 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 44-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21964, catechol O-methyltransferase

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Non-polymers , 5 types, 254 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Chemical ChemComp-DNC / 3,5-DINITROCATECHOL


Mass: 200.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4N2O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: AMMONIUM SULPHATE, CHES, PH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.5→37.88 Å / Num. obs: 32181 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.47 % / Biso Wilson estimate: 21.029 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.109 / Χ2: 1.038 / Net I/σ(I): 8.53 / Num. measured all: 111776
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.540.6741.264697242619470.5970.86380.3
1.54-1.580.5711.676062233221720.7050.70693.1
1.58-1.630.58127688231422870.7760.69198.8
1.63-1.680.4832.527765223222220.8340.5799.6
1.68-1.730.4162.827789220121890.8980.4999.5
1.73-1.790.323.817390207520640.9320.37699.5
1.79-1.860.2724.497311201220090.9570.31999.9
1.86-1.940.2116.017110195019400.9540.24799.5
1.94-2.020.1737.156827186218590.9750.20399.8
2.02-2.120.1398.956619179417920.9810.16399.9
2.12-2.240.12210.46282170516940.9840.14399.4
2.24-2.370.10312.126031163416270.9880.12199.6
2.37-2.540.08813.715489150414960.990.10499.5
2.54-2.740.0814.835057138813790.9920.09399.4
2.74-30.0716.544829133613290.9930.08299.5
3-3.350.05619.894115116911620.9950.06699.4
3.35-3.870.04622.153682105510490.9960.05499.4
3.87-4.740.04223.8531438938870.9970.04999.3
4.74-6.710.03723.6724966886830.9980.04399.3
6.71-37.880.03325.6613944053940.9990.03997.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0057refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.5→37.88 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.846 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.088
Details: there is a piece of unmodelled density close to the ligand binding site. nature of this density is unknown. clear density for ligands SAM and DNC.
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 1512 5.1 %RANDOM
Rwork0.1673 ---
obs0.1694 28358 90.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 46.74 Å2 / Biso mean: 12.995 Å2 / Biso min: 6.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20.88 Å2
2---0.04 Å20 Å2
3---1.35 Å2
Refinement stepCycle: final / Resolution: 1.5→37.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 43 250 1963
Biso mean--10.42 29.51 -
Num. residues----214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221788
X-RAY DIFFRACTIONr_bond_other_d0.0010.021175
X-RAY DIFFRACTIONr_angle_refined_deg1.6532.0022434
X-RAY DIFFRACTIONr_angle_other_deg0.9932893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5645224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93625.06379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25415309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.715159
X-RAY DIFFRACTIONr_chiral_restr0.1030.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211979
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02325
X-RAY DIFFRACTIONr_mcbond_it0.9841.51095
X-RAY DIFFRACTIONr_mcbond_other0.3071.5442
X-RAY DIFFRACTIONr_mcangle_it1.68121770
X-RAY DIFFRACTIONr_scbond_it2.6833693
X-RAY DIFFRACTIONr_scangle_it4.2634.5660
LS refinement shellResolution: 1.496→1.535 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 75 -
Rwork0.299 1330 -
all-1405 -
obs--57.77 %

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