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- PDB-3e2t: The catalytic domain of chicken tryptophan hydroxylase 1 with bou... -

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Basic information

Entry
Database: PDB / ID: 3e2t
TitleThe catalytic domain of chicken tryptophan hydroxylase 1 with bound tryptophan
ComponentsTryptophan 5-hydroxylase 1
KeywordsOXIDOREDUCTASE / aromatic amino acid hydroxylase tryptophan binding iron binding / Iron / Metal-binding / Monooxygenase / Phosphoprotein / Serotonin biosynthesis
Function / homology
Function and homology information


regulation of hemostasis / tryptophan 5-monooxygenase / tryptophan 5-monooxygenase activity / aromatic amino acid metabolic process / serotonin biosynthetic process / platelet degranulation / neuron projection / iron ion binding
Similarity search - Function
Tryptophan 5-monooxygenase / Tryptophan 5-hydroxylase, catalytic domain / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Tyrosine 3-monooxygenase-like / ACT domain / 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 ...Tryptophan 5-monooxygenase / Tryptophan 5-hydroxylase, catalytic domain / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Tyrosine 3-monooxygenase-like / ACT domain / 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. / ACT domain profile. / ACT domain / ACT-like domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / IMIDAZOLE / TRIETHYLENE GLYCOL / TRYPTOPHAN / Tryptophan 5-hydroxylase 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsWindahl, M.S. / Petersen, C.R. / Christensen, H.E.C. / Harris, P.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal structure of tryptophan hydroxylase with bound amino acid substrate
Authors: Windahl, M.S. / Petersen, C.R. / Christensen, H.E.M. / Harris, P.
History
DepositionAug 6, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / pdbx_struct_special_symmetry / 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.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 / _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: Tryptophan 5-hydroxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8647
Polymers36,1381
Non-polymers7266
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Tryptophan 5-hydroxylase 1
hetero molecules

A: Tryptophan 5-hydroxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,72714
Polymers72,2762
Non-polymers1,45112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4790 Å2
ΔGint-55 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.000, 155.300, 61.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-4-

SO4

21A-523-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Tryptophan 5-hydroxylase 1 / Tryptophan 5-monooxygenase 1


Mass: 36138.180 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP residues 101-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Strain: White leghorn / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P70080, tryptophan 5-monooxygenase

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Non-polymers , 6 types, 225 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M imidazole malate, 22.5% PEG 10000, pH 8.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 2007
RadiationMonochromator: Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→48.34 Å / Num. all: 30028 / Num. obs: 30024 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 22.612 Å2 / Rmerge(I) obs: 0.145 / Rsym value: 0.146 / Net I/σ(I): 13.84
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 30292 / Num. unique all: 4233 / Num. unique obs: 4233 / Rsym value: 0.547 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PAH

1pah


Resolution: 1.9→48.34 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.156 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.881 / SU B: 3.148 / SU ML: 0.093 / SU R Cruickshank DPI: 0.142 / SU Rfree: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1502 5 %RANDOM
Rwork0.182 ---
all0.1842 30024 --
obs0.184 30022 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.33 Å2 / Biso mean: 17.265 Å2 / Biso min: 4.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 46 219 2811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222663
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9843605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2455321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85523.415123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85515453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4131517
X-RAY DIFFRACTIONr_chiral_restr0.0930.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022041
X-RAY DIFFRACTIONr_nbd_refined0.2140.31158
X-RAY DIFFRACTIONr_nbtor_refined0.3150.51815
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.5333
X-RAY DIFFRACTIONr_metal_ion_refined0.0560.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.335
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.524
X-RAY DIFFRACTIONr_mcbond_it1.14921629
X-RAY DIFFRACTIONr_mcangle_it1.77932576
X-RAY DIFFRACTIONr_scbond_it1.16321175
X-RAY DIFFRACTIONr_scangle_it1.75731028
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 110 -
Rwork0.245 2084 -
all-2194 -
obs--100 %

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