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- PDB-4pgg: Caffeic acid O-methyltransferase from Sorghum bicolor -

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Basic information

Entry
Database: PDB / ID: 4pgg
TitleCaffeic acid O-methyltransferase from Sorghum bicolor
ComponentsCaffeic acid O-methyltransferase
KeywordsTRANSFERASE / SAM-dependent O-methyltransferase
Function / homology
Function and homology information


: / quercetin 3-O-methyltransferase activity / myricetin 3'-O-methyltransferase activity / acetylserotonin O-methyltransferase activity / caffeate O-methyltransferase activity / flavonol biosynthetic process / mucilage biosynthetic process involved in seed coat development / seed oilbody biogenesis / caffeate O-methyltransferase / response to mannitol ...: / quercetin 3-O-methyltransferase activity / myricetin 3'-O-methyltransferase activity / acetylserotonin O-methyltransferase activity / caffeate O-methyltransferase activity / flavonol biosynthetic process / mucilage biosynthetic process involved in seed coat development / seed oilbody biogenesis / caffeate O-methyltransferase / response to mannitol / regulation of anthocyanin metabolic process / melatonin biosynthetic process / lignin biosynthetic process / regulation of stomatal closure / serotonin metabolic process / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / response to osmotic stress / biosynthetic process / circadian rhythm / methylation / protein dimerization activity / nucleus / cytoplasm
Similarity search - Function
Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylases family 2 signature 2. / Plant methyltransferase dimerisation / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylases family 2 signature 2. / Plant methyltransferase dimerisation / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Caffeic acid O-methyltransferase
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.015 Å
AuthorsGreen, A.R. / Lewis, K.M. / Kang, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 102114 United States
CitationJournal: Plant Physiol. / Year: 2014
Title: Determination of the Structure and Catalytic Mechanism of Sorghum bicolor Caffeic Acid O-Methyltransferase and the Structural Impact of Three brown midrib12 Mutations.
Authors: Green, A.R. / Lewis, K.M. / Barr, J.T. / Jones, J.P. / Lu, F. / Ralph, J. / Vermerris, W. / Sattler, S.E. / Kang, C.
History
DepositionMay 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_symm_contact / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_keywords.text
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caffeic acid O-methyltransferase
B: Caffeic acid O-methyltransferase


Theoretical massNumber of molelcules
Total (without water)78,8642
Polymers78,8642
Non-polymers00
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-64 kcal/mol
Surface area29670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.232, 96.286, 124.282
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 Caffeic acid O-methyltransferase


Mass: 39432.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: Sb07g003860, SORBIDRAFT_07g003860 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: C5YH12, caffeate O-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.07M Bis-Tris propane, 0.03M Citric acid, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2013
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 58382 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.086 / Χ2: 3.692 / Net I/av σ(I): 43.102 / Net I/σ(I): 14 / Num. measured all: 405174
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.01-2.045.60.54427550.78996.7
2.04-2.085.90.46428991.16698.7
2.08-2.126.30.39428410.95899.2
2.12-2.176.80.33928541.04799.1
2.17-2.2170.32229121.16799.6
2.21-2.267.10.28628642.1899.6
2.26-2.327.10.24828931.49799.7
2.32-2.387.10.21328931.66399.8
2.38-2.457.10.18529261.92699.8
2.45-2.537.20.16729092.19499.7
2.53-2.627.20.15229082.58499.9
2.62-2.737.20.13729073.1799.9
2.73-2.857.20.12229253.52999.9
2.85-37.20.11329344.266100
3-3.197.30.10129644.951100
3.19-3.447.30.0929295.96100
3.44-3.787.20.08629537.16599.9
3.78-4.337.10.07929667.91899.6
4.33-5.456.90.06430037.02399.3
5.45-506.80.049314710.23699

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.015→38.058 Å / FOM work R set: 0.8408 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 2000 3.43 %
Rwork0.175 56312 -
obs0.1764 58312 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.49 Å2 / Biso mean: 41.84 Å2 / Biso min: 20.81 Å2
Refinement stepCycle: final / Resolution: 2.015→38.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5534 0 0 480 6014
Biso mean---47.17 -
Num. residues----720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065682
X-RAY DIFFRACTIONf_angle_d0.917712
X-RAY DIFFRACTIONf_chiral_restr0.039854
X-RAY DIFFRACTIONf_plane_restr0.004998
X-RAY DIFFRACTIONf_dihedral_angle_d13.3072058
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.015-2.0650.2911330.2443742387594
2.065-2.12080.30731390.22423934407399
2.1208-2.18320.25361420.21933980412299
2.1832-2.25360.30931420.226540044146100
2.2536-2.33420.27561410.206639794120100
2.3342-2.42760.2521430.189840094152100
2.4276-2.53810.2191430.191740314174100
2.5381-2.67190.24451420.192340194161100
2.6719-2.83920.25531440.195440414185100
2.8392-3.05830.24551430.201640324175100
3.0583-3.36590.2131450.189640854230100
3.3659-3.85260.19651450.171140924237100
3.8526-4.85230.17541460.13894093423999
4.8523-38.06460.18321520.14664271442399

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