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

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Basic information

Entry
Database: PDB / ID: 4kib
TitleCrystal structure of methyltransferase from Streptomyces hygroscopicus complexed with S-adenosyl-L-homocysteine and methylphenylpyruvic 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(3R)-2-oxo-3-phenylbutanoic acid / : / (2R)-2-hydroxy-3-phenylpropanoic acid / S-ADENOSYL-L-HOMOCYSTEINE / Phenylpyruvate C(3)-methyltransferase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_leaving_atom_flag / _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 2.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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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)81,41415
Polymers79,6452
Non-polymers1,77013
Water11,259625
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-48 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.332, 78.062, 138.257
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: 39822.340 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 , 6 types, 638 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-56D / (3R)-2-oxo-3-phenylbutanoic acid


Mass: 178.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O3
#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.: 5 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.56 %
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: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9787, 0.9789, 0.9635
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2012
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.97891
30.96351
ReflectionResolution: 2→30 Å / Num. all: 45227 / Num. obs: 45227 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.07 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
CRANKphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→26.39 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.319 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.212 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25615 2414 5.1 %RANDOM
Rwork0.19809 ---
obs0.20108 45227 99.56 %-
all-45227 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.675 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å2-0 Å2
2--0.32 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2→26.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5200 0 109 625 5934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195426
X-RAY DIFFRACTIONr_bond_other_d0.0010.025042
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9677346
X-RAY DIFFRACTIONr_angle_other_deg0.7873.00111515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.715666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54622.659267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27915791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3461556
X-RAY DIFFRACTIONr_chiral_restr0.0770.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021360
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 175 -
Rwork0.267 3217 -
obs--98.01 %

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