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- PDB-3zgj: S221M V223F Y359A mutant of 4-Hydroxymandelate synthase from Stre... -

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Basic information

Entry
Database: PDB / ID: 3zgj
TitleS221M V223F Y359A mutant of 4-Hydroxymandelate synthase from Streptomyces coelicolor
Components4-HYDROXYPHENYLPYRUVIC ACID DIOXYGENASE
KeywordsOXIDOREDUCTASE / DIOXYGENASE / NON-HEME IRON OXYGENASE / BENZYLIC HYDROXYLATION
Function / homology
Function and homology information


4-hydroxyphenylpyruvate dioxygenase activity / tyrosine catabolic process / metal ion binding
Similarity search - Function
4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase, C-terminal / 4-hydroxyphenylpyruvate dioxygenase, N-terminal / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase ...4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase, C-terminal / 4-hydroxyphenylpyruvate dioxygenase, N-terminal / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / (R)-MANDELIC ACID / Putative 4-hydroxyphenylpyruvic acid dioxygenase
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPratter, S. / Straganz, G. / Grogan, G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Inversion of Enantioselectivity of a Mononuclear Non-Heme Iron(II)-Dependent Hydroxylase by Tuning the Interplay of Metal Center Geometry and Protein Structure
Authors: Pratter, S. / Konstantinovics, C. / Digiuro, C.L.M. / Leitner, E. / Kumar, D. / De Visser, S.P. / Grogan, G. / Straganz, G.
History
DepositionDec 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: 4-HYDROXYPHENYLPYRUVIC ACID DIOXYGENASE
B: 4-HYDROXYPHENYLPYRUVIC ACID DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8966
Polymers80,4742
Non-polymers4224
Water9,566531
1
A: 4-HYDROXYPHENYLPYRUVIC ACID DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4483
Polymers40,2371
Non-polymers2112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-HYDROXYPHENYLPYRUVIC ACID DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4483
Polymers40,2371
Non-polymers2112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.870, 122.870, 54.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein 4-HYDROXYPHENYLPYRUVIC ACID DIOXYGENASE / 4-HYDROXYMANDELATE SYNTHASE


Mass: 40236.902 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Strain: A3(2) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z4X7, 4-hydroxymandelate synthase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-RMN / (R)-MANDELIC ACID


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSER221MET VAL223PHE TYR359ALA MUTATIONS

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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: 2.54 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 8.5
Details: 1 MICROLITRE 10 MG ML-1 HMS VARIANT, PREINCUBATED WITH 1.25 MM COCL2 AND 2.5 MM R-MANDELATE) PLUS 1 MICROLITRE MOTHER LIQUOR. THE BEST CRYSTALS WERE ROUTINELY OBTAINED IN CRYSTAL DROPS ...Details: 1 MICROLITRE 10 MG ML-1 HMS VARIANT, PREINCUBATED WITH 1.25 MM COCL2 AND 2.5 MM R-MANDELATE) PLUS 1 MICROLITRE MOTHER LIQUOR. THE BEST CRYSTALS WERE ROUTINELY OBTAINED IN CRYSTAL DROPS CONTAINING 0.05 M TRIS/CL PH 9.0, 0.1 M MGCL2, 7.5% (W/V) PEG 4K AND 2.5% (V/V) 2-METHYL-1,4-PENTANEDIOL.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→61.44 Å / Num. obs: 57014 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6
Reflection shellResolution: 1.95→2.01 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R5V

2r5v


Resolution: 1.95→54.95 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.268 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21504 3049 5.1 %RANDOM
Rwork0.17505 ---
obs0.17711 57014 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.805 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2---0.68 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.95→54.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5051 0 24 531 5606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0195197
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.9677090
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11422.669236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57615727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1291549
X-RAY DIFFRACTIONr_chiral_restr0.1560.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214083
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4943.2492675
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.6834.8373332
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5943.5742522
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 196 -
Rwork0.219 4191 -
obs--100 %

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