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- PDB-3tcy: Crystallographic structure of phenylalanine hydroxylase from Chro... -

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Basic information

Entry
Database: PDB / ID: 3tcy
TitleCrystallographic structure of phenylalanine hydroxylase from Chromobacterium violaceum (cPAH) bound to phenylalanine in a site distal to the active site
ComponentsPhenylalanine-4-hydroxylase
KeywordsOXIDOREDUCTASE / PHENYLALANINE HYDROXYLASE / SUBSTRATE-PROTEIN COMPLEX / DISTAL SITE / phenylalanine bound structure
Function / homology
Function and homology information


phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / L-phenylalanine catabolic process / iron ion binding
Similarity search - Function
Phenylalanine-4-hydroxylase, monomeric form / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, iron/copper binding site / Biopterin-dependent aromatic amino acid hydroxylases signature. / 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 ...Phenylalanine-4-hydroxylase, monomeric form / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, iron/copper binding site / Biopterin-dependent aromatic amino acid hydroxylases signature. / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PHENYLALANINE / Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRonau, J.A. / Abu-Omar, M.M. / Das, C.
CitationJournal: Eur.Biophys.J. / Year: 2013
Title: An additional substrate binding site in a bacterial phenylalanine hydroxylase.
Authors: Ronau, J.A. / Paul, L.N. / Fuchs, J.E. / Corn, I.R. / Wagner, K.T. / Liedl, K.R. / Abu-Omar, M.M. / Das, C.
History
DepositionAug 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Sep 13, 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_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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry / _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: Phenylalanine-4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4476
Polymers34,0391
Non-polymers4075
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.674, 38.281, 47.736
Angle α, β, γ (deg.)76.65, 73.03, 85.69
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Phenylalanine-4-hydroxylase / PAH / Phe-4-monooxygenase


Mass: 34039.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: phhA, CV_3180 / Plasmid: PGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P30967, phenylalanine 4-monooxygenase
#2: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 1.83 Å3/Da / Density % sol: 32.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Na-HEPES, 0.001M Magnesium chloride hexahydrate, 0.005M Nickel (II) chloride hexahydrate, 15% w/v PEG 3,350, 0.1M hexammine cobalt (II) chloride, 1.0M guanidine hydrochloride, pH 7.0, ...Details: 0.1M Na-HEPES, 0.001M Magnesium chloride hexahydrate, 0.005M Nickel (II) chloride hexahydrate, 15% w/v PEG 3,350, 0.1M hexammine cobalt (II) chloride, 1.0M guanidine hydrochloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 27, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 33011 / Num. obs: 31363 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 26.2
Reflection shellResolution: 1.55→1.58 Å / % possible all: 84.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LTU

1ltu


Resolution: 1.55→37.25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.286 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20698 1647 5 %RANDOM
Rwork0.16266 ---
obs0.16488 31360 94.78 %-
all-33090 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.555 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0.01 Å20 Å2
2--0 Å2-0.01 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 22 214 2457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222311
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9683147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2985278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1723.604111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35315358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8281515
X-RAY DIFFRACTIONr_chiral_restr0.0910.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211805
X-RAY DIFFRACTIONr_mcbond_it1.0251.51391
X-RAY DIFFRACTIONr_mcangle_it1.67122245
X-RAY DIFFRACTIONr_scbond_it2.5493920
X-RAY DIFFRACTIONr_scangle_it3.8244.5901
X-RAY DIFFRACTIONr_rigid_bond_restr1.44732311
X-RAY DIFFRACTIONr_sphericity_free4.0463216
X-RAY DIFFRACTIONr_sphericity_bonded2.80832247
LS refinement shellResolution: 1.55→1.594 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 115 -
Rwork0.222 2049 -
obs--82.13 %
Refinement TLS params.Method: refined / Origin x: 0.6409 Å / Origin y: 0.1694 Å / Origin z: -0.2975 Å
111213212223313233
T0.0171 Å2-0.0077 Å2-0.0044 Å2-0.0108 Å2-0.0013 Å2--0.0354 Å2
L0.9141 °2-0.1044 °2-0.2325 °2-0.5171 °20.2008 °2--1.0229 °2
S-0.0093 Å °-0.0174 Å °0.0471 Å °0.0087 Å °0.0335 Å °0.023 Å °0.0274 Å °0.0635 Å °-0.0241 Å °

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