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- PDB-7vgm: Crystal structure of Phenylalanine hydroxylase from Bacillus cere... -

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Basic information

Entry
Database: PDB / ID: 7vgm
TitleCrystal structure of Phenylalanine hydroxylase from Bacillus cereus ATCC 14579
ComponentsPhenylalanine-4-hydroxylase
KeywordsMETAL BINDING PROTEIN / phenylalanine hydroxylase
Function / homology
Function and homology information


phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / iron ion binding
Similarity search - Function
Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, C-terminal / Aromatic amino acid monoxygenase, C-terminal domain superfamily / Aromatic amino acid hydroxylase superfamily / Biopterin-dependent aromatic amino acid hydroxylase / Biopterin-dependent aromatic amino acid hydroxylase family profile.
Similarity search - Domain/homology
ACETIC ACID / : / DI(HYDROXYETHYL)ETHER / Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.27 Å
AuthorsPark, J. / Kim, K.-J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural studies of a novel auxiliary-domain-containing phenylalanine hydroxylase from Bacillus cereus ATCC 14579.
Authors: Park, J. / Hong, J. / Seok, J. / Hong, H. / Seo, H. / Kim, K.J.
History
DepositionSep 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylalanine-4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,62818
Polymers65,3631
Non-polymers1,26517
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-9 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.273, 93.698, 95.676
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phenylalanine-4-hydroxylase


Mass: 65362.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Strain: ATCC 14579 / Gene: BC_4352 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q818B4, phenylalanine 4-monooxygenase

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Non-polymers , 6 types, 368 molecules

#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Polyethylene glycol 3,350, Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 17, 2020
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 32319 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.062 / Rrim(I) all: 0.122 / Χ2: 2.639 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.28-2.3230.35815420.8770.2280.4271.70697.8
2.32-2.363.50.34715980.90.2110.4071.77699.4
2.36-2.413.70.31715930.9250.1890.371.77699.7
2.41-2.463.70.32116030.9150.1920.3761.86599.8
2.46-2.513.70.27116060.9520.1610.3161.94399.9
2.51-2.573.70.23815970.950.140.2771.92999.8
2.57-2.633.70.22816200.9450.1350.2661.99999.8
2.63-2.73.70.18815860.9750.110.2182.10299.7
2.7-2.783.70.18216030.9690.1070.2122.12299.6
2.78-2.873.70.16116260.9740.0950.1882.13199.8
2.87-2.983.60.13916120.9810.0820.1622.20399.4
2.98-3.093.60.12216060.9880.0710.1412.24599.6
3.09-3.243.60.11216230.9880.0650.132.44499.4
3.24-3.413.60.09916050.9870.0570.1152.64399.3
3.41-3.623.60.08616210.9890.050.12.84599.4
3.62-3.93.60.07516280.990.0440.0873.26499.4
3.9-4.293.60.07216290.9910.0420.0843.67199
4.29-4.913.60.0716450.990.0410.0824.33999
4.91-6.193.50.0716630.9890.0420.0824.198.8
6.19-503.30.07317130.9880.0460.0875.69195.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
AutoSolphasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.27→33.49 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.383 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 1570 4.9 %RANDOM
Rwork0.1732 ---
obs0.1764 30701 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.48 Å2 / Biso mean: 35.878 Å2 / Biso min: 16.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--3.57 Å2-0 Å2
3----3.6 Å2
Refinement stepCycle: final / Resolution: 2.27→33.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4425 0 80 351 4856
Biso mean--50.31 38.49 -
Num. residues----571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134584
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174326
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.6396204
X-RAY DIFFRACTIONr_angle_other_deg1.2741.579989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6095570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25924.279215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23615751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2541514
X-RAY DIFFRACTIONr_chiral_restr0.0660.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02968
LS refinement shellResolution: 2.273→2.332 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 113 -
Rwork0.243 2097 -
all-2210 -
obs--93.53 %

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