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

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Basic information

Entry
Database: PDB / ID: 4kig
TitleCrystal structure of methyltransferase from Streptomyces hygroscopicus complexed with 4-hydroxyphenylpyruvic 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-(4-HYDROXYPHENYL)PROPANOIC ACID / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / : / Phenylpyruvate C(3)-methyltransferase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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_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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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

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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)79,99817
Polymers78,8012
Non-polymers1,19715
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-141 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.485, 81.145, 137.422
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 , 5 types, 373 molecules

#2: Chemical ChemComp-ENO / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / HPP


Mass: 180.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O4
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-34H / (2R)-2-HYDROXY-3-(4-HYDROXYPHENYL)PROPANOIC ACID


Mass: 182.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O4
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
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: BL13C1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2013
RadiationMonochromator: Horizontally Focusing Single Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 23694 / Num. obs: 23694 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.4→2.49 Å / % possible all: 96

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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: 2.4→25.88 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.778 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.861 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24816 1271 5.1 %RANDOM
Rwork0.16803 ---
obs0.17221 23694 92.66 %-
all-23694 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.018 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å2-0 Å2
2---0.74 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 63 358 5591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195342
X-RAY DIFFRACTIONr_bond_other_d0.0020.024972
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9497228
X-RAY DIFFRACTIONr_angle_other_deg0.829311350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2275662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40422.632266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5315828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.971556
X-RAY DIFFRACTIONr_chiral_restr0.0850.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021346
LS refinement shellResolution: 2.4→2.456 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 64 -
Rwork0.201 1592 -
obs--84.27 %

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