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- PDB-7cvx: Crystal structure of Catechol o-methyl transferase (COMT) from Ni... -

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Basic information

Entry
Database: PDB / ID: 7cvx
TitleCrystal structure of Catechol o-methyl transferase (COMT) from Niastella koreensis
ComponentsO-methyltransferase family 3
KeywordsTRANSFERASE / Catechol o-methyl transferase / Mannheimia succiniciproducens / succinate production / TCA cycle / LYASE
Function / homology
Function and homology information


catechol O-methyltransferase / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / metal ion binding
Similarity search - Function
: / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
3,4-DIHYDROXYBENZOIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesNiastella koreensis GR20-10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKim, B. / Lee, S.H. / Kim, K.-J.
CitationJournal: To Be Published
Title: Structural and Biochemical analysis of FumaraseC from Mannheimia succiniciproducens
Authors: Kim, B. / Lee, S.H. / Kim, K.J.
History
DepositionAug 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: O-methyltransferase family 3
B: O-methyltransferase family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4759
Polymers50,2572
Non-polymers1,2187
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-52 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.871, 42.778, 98.606
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein O-methyltransferase family 3


Mass: 25128.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Niastella koreensis GR20-10 (bacteria) / Strain: GR20-10 / Gene: Niako_0425 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: G8T6H8

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Non-polymers , 5 types, 298 molecules

#2: 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
#3: Chemical ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 18% PEG8000, 0.1M MES/Sodium hydroxide pH 6.0 and 0.2 M Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 45847 / % possible obs: 95.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.058 / Rrim(I) all: 0.135 / Χ2: 9.729 / Net I/σ(I): 16.6 / Num. measured all: 228053
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.735.20.31422720.870.150.3494.15597.6
1.73-1.765.10.28423080.8950.1360.3164.83997.7
1.76-1.795.10.26822580.9060.1290.2985.06796.3
1.79-1.8350.23823170.9250.1150.2655.24298.2
1.83-1.8750.22822900.9320.110.2545.88695.9
1.87-1.914.90.21322650.9280.1040.2386.78496.7
1.91-1.9650.19222420.9390.0940.2157.34795.2
1.96-2.024.80.18223040.940.0910.2057.65896.2
2.02-2.074.90.1722220.950.0840.198.63894.6
2.07-2.144.80.15922730.9530.0790.1789.34294.7
2.14-2.224.80.15422410.960.0750.1729.96194.8
2.22-2.314.80.14622490.9650.0710.16310.94394.5
2.31-2.414.80.13922630.9680.0690.15611.44994.9
2.41-2.544.80.13522720.9690.0670.15111.03494.2
2.54-2.74.70.12822670.9740.0630.14312.39695
2.7-2.914.70.11922890.9690.0590.13412.96494.9
2.91-3.24.90.11222940.9810.0540.12514.03795
3.2-3.665.20.10323880.9830.0490.11416.08597.5
3.66-4.615.40.10224320.9820.0480.11317.28398
4.61-505.40.09524010.9840.0440.10512.06591.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N5D

5n5d


Resolution: 1.7→30.82 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.892 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 2276 5 %RANDOM
Rwork0.1689 ---
obs0.171 43542 95.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.12 Å2 / Biso mean: 17.181 Å2 / Biso min: 5.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.46 Å2
Refinement stepCycle: final / Resolution: 1.7→30.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 82 291 3725
Biso mean--20.47 27.66 -
Num. residues----439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133483
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173281
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.6374733
X-RAY DIFFRACTIONr_angle_other_deg1.4681.5737609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9755436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35423.576165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2315579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2231518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02664
LS refinement shellResolution: 1.701→1.745 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 146 -
Rwork0.187 2931 -
all-3077 -
obs--88.12 %

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