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- PDB-2r5v: Hydroxymandelate Synthase Crystal Structure -

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Basic information

Entry
Database: PDB / ID: 2r5v
TitleHydroxymandelate Synthase Crystal Structure
ComponentsPCZA361.1
KeywordsOXIDOREDUCTASE / dioxygenase / non-heme iron / vancomycin
Function / homology
Function and homology information


4-hydroxymandelate synthase / 4-hydroxymandelate synthase activity / aromatic amino acid metabolic process / vancomycin biosynthetic process / 4-hydroxyphenylpyruvate dioxygenase activity / iron ion binding
Similarity search - Function
Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal / 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. ...Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal / 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
: / (2S)-hydroxy(4-hydroxyphenyl)ethanoic acid / PHOSPHATE ION / 4-hydroxymandelate synthase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsBrownlee, J.M. / He, P. / Moran, G.R. / Harrison, D.H.T.
CitationJournal: Biochemistry / Year: 2008
Title: Two roads diverged: the structure of hydroxymandelate synthase from Amycolatopsis orientalis in complex with 4-hydroxymandelate.
Authors: Brownlee, J. / He, P. / Moran, G.R. / Harrison, D.H.
History
DepositionSep 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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Assembly

Deposited unit
A: PCZA361.1
B: PCZA361.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3047
Polymers76,7552
Non-polymers5495
Water3,909217
1
A: PCZA361.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6043
Polymers38,3771
Non-polymers2272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PCZA361.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6994
Polymers38,3771
Non-polymers3223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.369, 106.369, 75.951
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein PCZA361.1


Mass: 38377.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Gene: HmaS / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O52791, 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-HHH / (2S)-hydroxy(4-hydroxyphenyl)ethanoic acid


Mass: 168.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.8 Å3/Da / Density % sol: 56.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16-20% PEG 3350, 100mM phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.5957 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5957 Å / Relative weight: 1
ReflectionRedundancy: 5.6 % / Av σ(I) over netI: 15 / Number: 511014 / Rmerge(I) obs: 0.082 / Χ2: 1.62 / D res high: 2.15 Å / D res low: 50 Å / Num. obs: 90963 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.635099.910.0552.0615.7
3.684.6310010.0652.4125.7
3.213.6810010.0842.5855.7
2.923.2110010.091.8175.7
2.712.9210010.1191.4495.7
2.552.7110010.1631.2215.6
2.422.5510010.2121.0985.6
2.322.4210010.2941.0665.6
2.232.3210010.4021.1375.5
2.152.2310010.5321.2545.5
ReflectionResolution: 2.15→50 Å / Num. obs: 38006 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.617 / Net I/σ(I): 15
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 4.2 / Num. unique all: 9187 / Χ2: 1.254 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Co39.6510.1830.6320.9960.538
2Co30.1670.6990.780.1560.501

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→47.57 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.689 / SU ML: 0.141 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1898 5 %RANDOM
Rwork0.174 ---
obs0.177 37953 99.85 %-
all-38010 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.782 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2--0.89 Å20 Å2
3----1.77 Å2
Refine analyzeLuzzati coordinate error obs: 0.253 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5047 0 31 217 5295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0215174
X-RAY DIFFRACTIONr_angle_refined_deg1.9491.9397043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0335670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89124.268239
X-RAY DIFFRACTIONr_chiral_restr0.14715748
X-RAY DIFFRACTIONr_gen_planes_refined0.0091528
X-RAY DIFFRACTIONr_nbd_refined0.2110.2809
X-RAY DIFFRACTIONr_nbtor_refined0.3060.024018
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.22180
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.23482
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.2256
X-RAY DIFFRACTIONr_mcbond_it1.3180.21
X-RAY DIFFRACTIONr_mcangle_it2.2220.242
X-RAY DIFFRACTIONr_scbond_it3.320.213
X-RAY DIFFRACTIONr_scangle_it5.0841.53420
LS refinement shellResolution: 2.3→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 142 -
Rwork0.211 2599 -
all-2741 -
obs-2599 98.21 %

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