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- PDB-4kic: Crystal structure of methyltransferase from Streptomyces hygrosco... -

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Basic information

Entry
Database: PDB / ID: 4kic
TitleCrystal structure of methyltransferase from Streptomyces hygroscopicus complexed with S-adenosyl-L-methionine and phenylpyruvic acid
ComponentsMethyltransferase MppJ
KeywordsTRANSFERASE / Rossmann Fold / Methyltransferase / SAM Binding PPY Binding
Function / homology
Function and homology information


phenylpyruvate C3-methyltransferase / antibiotic biosynthetic process / methyltransferase activity / methylation
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / 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 ...Methyltransferase domain 25 / Methyltransferase domain / 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
: / (2R)-2-hydroxy-3-phenylpropanoic acid / IODIDE ION / 3-PHENYLPYRUVIC ACID / S-ADENOSYLMETHIONINE / Phenylpyruvate C(3)-methyltransferase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsLiu, Y.C. / Zou, X.W. / Chan, H.C. / Huang, C.J. / Li, T.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure and mechanism of a nonhaem-iron SAM-dependent C-methyltransferase and its engineering to a hydratase and an O-methyltransferase
Authors: Zou, X.W. / Liu, Y.C. / Hsu, N.S. / Huang, C.J. / Lyu, S.Y. / Chan, H.C. / Chang, C.Y. / Yeh, H.W. / Lin, K.H. / Wu, C.J. / Tsai, M.D. / Li, T.L.
History
DepositionMay 2, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase MppJ
B: Methyltransferase MppJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,01824
Polymers78,8012
Non-polymers2,21722
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-211 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.547, 93.498, 142.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 Methyltransferase MppJ


Mass: 39400.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: mppJ / Production host: Escherichia coli (E. coli) / References: UniProt: Q643C8

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Non-polymers , 7 types, 321 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-PPY / 3-PHENYLPYRUVIC ACID


Mass: 164.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O3
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-HF2 / (2R)-2-hydroxy-3-phenylpropanoic acid


Type: peptide-like / Mass: 166.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O3
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG3350, 0.2M sodium iodide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 24, 2010
RadiationMonochromator: Diffracted Beam Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.43→19 Å / Num. all: 27511 / Num. obs: 27511 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.43→2.54 Å / % possible all: 90.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERMRphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KIB

4kib


Resolution: 2.43→19 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.33 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.437 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23755 1478 5.1 %RANDOM
Rwork0.16729 ---
obs0.17103 27511 97.06 %-
all-27511 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.589 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-0 Å20 Å2
2--2.63 Å20 Å2
3----3.01 Å2
Refinement stepCycle: LAST / Resolution: 2.43→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5186 0 118 299 5603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195412
X-RAY DIFFRACTIONr_bond_other_d0.0010.025031
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.967326
X-RAY DIFFRACTIONr_angle_other_deg0.854311489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9835664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27222.659267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52115831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5141556
X-RAY DIFFRACTIONr_chiral_restr0.090.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021368
LS refinement shellResolution: 2.43→2.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 97 -
Rwork0.254 1879 -
obs--90.89 %

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