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- PDB-1sus: Crystal structure of alfalfa feruoyl coenzyme A 3-O-methyltransferase -

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Basic information

Entry
Database: PDB / ID: 1sus
TitleCrystal structure of alfalfa feruoyl coenzyme A 3-O-methyltransferase
ComponentsCaffeoyl-CoA O-methyltransferase
KeywordsTRANSFERASE / ROSSMANN FOLD / PROTEIN-COFACTOR-SUBSTRATE COMPLEX / O-METHYLTRANSFERASE
Function / homology
Function and homology information


caffeoyl-CoA O-methyltransferase / caffeoyl-CoA O-methyltransferase activity / lignin biosynthetic process / methylation / metal ion binding
Similarity search - Function
: / 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 / SINAPOYL COENZYME A / Caffeoyl-CoA O-methyltransferase
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsFerrer, J.-L. / Zubieta, C. / Dixon, R.A. / Noel, J.P.
CitationJournal: Plant Physiol. / Year: 2005
Title: Crystal Structures of Alfalfa Caffeoyl Coenzyme A 3-O-Methyltransferase
Authors: Ferrer, J.-L. / Zubieta, C. / Dixon, R.A. / Noel, J.P.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caffeoyl-CoA O-methyltransferase
B: Caffeoyl-CoA O-methyltransferase
C: Caffeoyl-CoA O-methyltransferase
D: Caffeoyl-CoA O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,81413
Polymers112,1454
Non-polymers2,6709
Water1,18966
1
A: Caffeoyl-CoA O-methyltransferase
C: Caffeoyl-CoA O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8937
Polymers56,0722
Non-polymers1,8215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-50 kcal/mol
Surface area19970 Å2
MethodPISA
2
B: Caffeoyl-CoA O-methyltransferase
hetero molecules

B: Caffeoyl-CoA O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9216
Polymers56,0722
Non-polymers8494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
3
D: Caffeoyl-CoA O-methyltransferase
hetero molecules

D: Caffeoyl-CoA O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9216
Polymers56,0722
Non-polymers8494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)60.854, 136.486, 332.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Caffeoyl-CoA O-methyltransferase / Trans-caffeoyl-CoA 3-O-methyltransferase / CCoAMT / CCoAOMT


Mass: 28036.178 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Gene: CCOMT / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q40313, caffeoyl-CoA O-methyltransferase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-SPF / SINAPOYL COENZYME A


Mass: 971.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H44N7O20P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, TAPS, calcium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97966, 0.97927, 0.97549
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 18, 2001
RadiationMonochromator: SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979661
20.979271
30.975491
ReflectionResolution: 2.7→25 Å / Num. all: 37858 / Num. obs: 37858 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 79.7 Å2 / Rsym value: 0.076 / Net I/σ(I): 19.6
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 1.44 % / Mean I/σ(I) obs: 0.92 / Rsym value: 0.335 / % possible all: 61.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
MLPHAREphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1789 5 %RANDOM
Rwork0.245 ---
all-35644 --
obs-35644 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.07 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 75.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.84 Å20 Å20 Å2
2---5.56 Å20 Å2
3---9.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7210 0 171 66 7447
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.26
LS refinement shellResolution: 2.7→2.87 Å
RfactorNum. reflection% reflection
Rfree0.395 228 -
Rwork0.386 3723 -
obs--61.7 %

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