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

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Basic information

Entry
Database: PDB / ID: 7cvv
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-ADENOSYLMETHIONINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesNiastella koreensis GR20-10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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
C: O-methyltransferase family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5816
Polymers75,3863
Non-polymers1,1953
Water23413
1
A: O-methyltransferase family 3
C: O-methyltransferase family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0544
Polymers50,2572
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-36 kcal/mol
Surface area17040 Å2
MethodPISA
2
B: O-methyltransferase family 3
hetero molecules

B: O-methyltransferase family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0544
Polymers50,2572
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3750 Å2
ΔGint-37 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.185, 93.181, 43.335
Angle α, β, γ (deg.)90.000, 104.120, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein O-methyltransferase family 3


Mass: 25128.637 Da / Num. of mol.: 3
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
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
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: Nov 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 21163 / % possible obs: 99 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.055 / Rrim(I) all: 0.138 / Χ2: 6.48 / Net I/σ(I): 15.7 / Num. measured all: 113566
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.544.20.31610710.770.1670.3593.30698.2
2.54-2.594.40.3110150.7680.1610.3513.62598.4
2.59-2.644.40.28710400.8410.1480.3243.13998.6
2.64-2.694.50.27310640.8990.1370.3073.46998.3
2.69-2.754.60.2510350.9140.1250.283.99298.9
2.75-2.824.70.22910530.9290.1130.2563.88898.5
2.82-2.894.70.21410550.9370.1050.243.81298.7
2.89-2.964.90.19910390.9470.0950.2223.95699
2.96-3.055.10.19210720.9620.0880.2124.60599.3
3.05-3.155.10.1810570.9620.0830.1995.2799.1
3.15-3.265.40.16710470.9690.0750.1835.72999
3.26-3.395.40.14710530.9810.0660.1616.62899.2
3.39-3.555.50.1510520.9770.0660.1647.7799.2
3.55-3.736.50.1310860.9830.0540.1418.06599.8
3.73-3.9760.12410530.9860.0520.1349.18399.2
3.97-4.276.40.11110800.9890.0460.1210.00699.5
4.27-4.76.50.09610480.9920.040.1049.53898.6
4.7-5.386.20.09310790.9930.0390.1017.69799.9
5.38-6.786.30.09610750.9920.040.1047.0799.9
6.78-506.30.0910890.9920.0380.09710.14798.3

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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: 2.52→31.08 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.631 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 1043 4.9 %RANDOM
Rwork0.1784 ---
obs0.1804 20120 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.37 Å2 / Biso mean: 36.014 Å2 / Biso min: 19.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å20.32 Å2
2---1.07 Å20 Å2
3---2.67 Å2
Refinement stepCycle: final / Resolution: 2.52→31.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5016 0 81 13 5110
Biso mean--41.49 37.08 -
Num. residues----657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135187
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174902
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.6367053
X-RAY DIFFRACTIONr_angle_other_deg1.2391.57311370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.46723.614249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.73715867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9691527
X-RAY DIFFRACTIONr_chiral_restr0.0630.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025799
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02987
LS refinement shellResolution: 2.52→2.582 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.281 77 -
Rwork0.239 1062 -
obs--71.5 %

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