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

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Basic information

Entry
Database: PDB / ID: 7cvw
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
S-ADENOSYL-L-HOMOCYSTEINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesNiastella koreensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)51,2598
Polymers50,2572
Non-polymers1,0026
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size-exclusive chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-56 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.689, 98.226, 101.773
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 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 (strain DSM 17620 / KACC 11465 / NBRC 106392 / GR20-10) (bacteria)
Strain: DSM 17620 / KACC 11465 / NBRC 106392 / GR20-10 / Gene: Niako_0425 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: G8T6H8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 42.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20% PEG4000, 20% 2-Propanol and 0.1M Sodium citrate pH 5.6

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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: Mar 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 63757 / % possible obs: 99.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Χ2: 2.526 / Net I/σ(I): 12.3 / Num. measured all: 394759
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.54-1.574.70.31331180.8260.1530.351.46999.1
1.57-1.64.90.29831160.8470.1420.3311.56299
1.6-1.635.10.27231450.8920.1270.3011.64499.2
1.63-1.665.20.25931410.910.120.2871.6599.1
1.66-1.695.30.24231240.9250.110.2671.67799.2
1.69-1.735.40.22831350.940.1030.2511.82499.2
1.73-1.785.60.19431860.970.0860.2131.86399.4
1.78-1.835.80.17931210.9740.0780.1961.94599.5
1.83-1.885.90.1631580.9780.0680.1742.05499.3
1.88-1.946.20.14431980.9840.060.1562.2199.8
1.94-2.016.40.12931480.9870.0530.142.42299.8
2.01-2.096.60.11431810.990.0460.1242.4499.8
2.09-2.196.80.10331790.9920.0410.1122.59399.8
2.19-2.370.09432030.9940.0370.1022.72899.8
2.3-2.4470.08831990.9940.0340.0952.82999.9
2.44-2.6370.08232180.9940.0320.0882.79499.9
2.63-2.97.20.07432400.9950.0290.082.94499.8
2.9-3.327.30.06932410.9960.0260.0743.17299.8
3.32-4.187.40.06332890.9970.0240.0684.08799.8
4.18-506.70.06234170.9950.0260.0684.14198.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N5D

5n5d


Resolution: 1.54→27.55 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.296 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 3366 5.3 %RANDOM
Rwork0.1739 ---
obs0.175 60347 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.87 Å2 / Biso mean: 13.533 Å2 / Biso min: 2.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0 Å2-0 Å2
2--0.21 Å2-0 Å2
3---0.41 Å2
Refinement stepCycle: final / Resolution: 1.54→27.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 0 66 159 3569
Biso mean--19.7 21.32 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0133466
X-RAY DIFFRACTIONr_bond_other_d0.0420.0173272
X-RAY DIFFRACTIONr_angle_refined_deg2.6631.6384708
X-RAY DIFFRACTIONr_angle_other_deg1.7091.5757594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7845436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.06223.614166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87915578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2241518
X-RAY DIFFRACTIONr_chiral_restr0.0770.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.023874
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02658
LS refinement shellResolution: 1.541→1.581 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 257 -
Rwork0.223 4340 -
all-4597 -
obs--98.12 %

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