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- PDB-1ltz: CRYSTAL STRUCTURE OF CHROMOBACTERIUM VIOLACEUM PHENYLALANINE HYDR... -

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Basic information

Entry
Database: PDB / ID: 1ltz
TitleCRYSTAL STRUCTURE OF CHROMOBACTERIUM VIOLACEUM PHENYLALANINE HYDROXYLASE, STRUCTURE HAS BOUND IRON (III) AND OXIDIZED COFACTOR 7,8-DIHYDROBIOPTERIN
ComponentsPHENYLALANINE-4-HYDROXYLASE
KeywordsOXIDOREDUCTASE / HYDROXYLASE / PHENYLALANINE / DIHYDROBIOPTERIN / BACTERIAL ENZYME
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
: / 7,8-DIHYDROBIOPTERIN / Phenylalanine-4-hydroxylase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference map / Resolution: 1.4 Å
AuthorsErlandsen, H. / Kim, J.Y. / Patch, M.G. / Han, A. / Volner, A. / Abu-Omar, M.M. / Stevens, R.C.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structural comparison of bacterial and human iron-dependent phenylalanine hydroxylases: similar fold, different stability and reaction rates.
Authors: Erlandsen, H. / Kim, J.Y. / Patch, M.G. / Han, A. / Volner, A. / Abu-Omar, M.M. / Stevens, R.C.
History
DepositionMay 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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_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

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Assembly

Deposited unit
A: PHENYLALANINE-4-HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9584
Polymers33,6281
Non-polymers3313
Water6,197344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.700, 67.860, 91.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PHENYLALANINE-4-HYDROXYLASE / PAH / Phe-4-monooxygenase / Phenylalaninase


Mass: 33627.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS / References: UniProt: P30967, phenylalanine 4-monooxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HBI / 7,8-DIHYDROBIOPTERIN


Mass: 239.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N5O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, NaCl, HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.65-1.90 Mammonium sulfate1reservoir
240-100 mM1reservoirNaCl
320 mMHEPES1reservoirpH7.5
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 54370 / Num. obs: 54730 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 28
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1910 / % possible all: 67.2
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 20 Å / Redundancy: 9-12 / Num. measured all: 54730 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 67.2 % / Rmerge(I) obs: 0.427

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Processing

Software
NameClassification
CNSrefinement
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: Difference map
Starting model: PDB ENTRY 1LTU

1ltu


Resolution: 1.4→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 5425 -RANDOM
Rwork0.159 ---
all-53429 --
obs-53429 92 %-
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 19 344 2565
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d2.05
Software
*PLUS
Name: 'CNS, SHELZ' / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.05
LS refinement shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.42 Å

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