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- PDB-2v27: Structure of the cold active phenylalanine hydroxylase from Colwe... -

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Basic information

Entry
Database: PDB / ID: 2v27
TitleStructure of the cold active phenylalanine hydroxylase from Colwellia psychrerythraea 34H
ComponentsPHENYLALANINE HYDROXYLASE
KeywordsOXIDOREDUCTASE / COLD ADAPTATION / TETRAHYDROBIOPTERIN / COLWELLIA PSYCHRERYTHRAEA / PHENYLALANINE HYDROXYLASE / STABILITY / FLEXIBILITY / ALKAPTONURIA
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-4-hydroxylase
Similarity search - Component
Biological speciesCOLWELLIA PSYCHRERYTHRAEA 34H (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLeiros, H.-K.S. / Pey, A.L. / Innselset, M. / Moe, E. / Leiros, I. / Steen, I.H. / Martinez, A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure of Phenylalanine Hydroxylase from Colwellia Psychrerythraea 34H, a Monomeric Cold Active Enzyme with Local Flexibility Around the Active Site and High Overall Stability.
Authors: Leiros, H.-K.S. / Pey, A.L. / Innselset, M. / Moe, E. / Leiros, I. / Steen, I.H. / Martinez, A.
History
DepositionJun 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
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 / _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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHENYLALANINE HYDROXYLASE
B: PHENYLALANINE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9286
Polymers63,6252
Non-polymers3044
Water13,836768
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.280, 86.020, 87.570
Angle α, β, γ (deg.)90.00, 97.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHENYLALANINE HYDROXYLASE


Mass: 31812.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) COLWELLIA PSYCHRERYTHRAEA 34H (bacteria)
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q47XN7, phenylalanine 4-monooxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / 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: 2.5 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.5
Details: 1.6-1.8 M AMMONIUM SULFATE, 100 MM NACL, 20 MM NAHEPESPH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→45 Å / Num. obs: 94151 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 12.65 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / % possible all: 87.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LTV

1ltv


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.313 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 4712 5 %RANDOM
Rwork0.162 ---
obs0.164 89373 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20.34 Å2
2---0.37 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 12 768 5142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224620
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.9636301
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9745580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.12624.019214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7415769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7921525
X-RAY DIFFRACTIONr_chiral_restr0.1150.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023583
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.22539
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23302
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2592
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1511.52884
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7724598
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.62231971
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7854.51703
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 355
Rwork0.236 6297

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