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- PDB-4v06: Crystal structure of human tryptophan hydroxylase 2 (TPH2), catal... -

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Basic information

Entry
Database: PDB / ID: 4v06
TitleCrystal structure of human tryptophan hydroxylase 2 (TPH2), catalytic domain
ComponentsTRYPTOPHAN 5-HYDROXYLASE 2Tryptophan hydroxylase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


tryptophan 5-monooxygenase / tryptophan 5-monooxygenase activity / Serotonin and melatonin biosynthesis / serotonin biosynthetic process / aromatic amino acid metabolic process / neuron projection / iron ion binding / cytosol
Similarity search - Function
Tryptophan 5-monooxygenase / Tryptophan 5-hydroxylase, catalytic domain / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Tyrosine 3-monooxygenase-like / 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 ...Tryptophan 5-monooxygenase / Tryptophan 5-hydroxylase, catalytic domain / Phenylalanine Hydroxylase / Aromatic amino acid hydroxylase / Tyrosine 3-monooxygenase-like / 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 / Tryptophan 5-hydroxylase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsKopec, J. / Oberholzer, A. / Fitzpatrick, F. / Newman, J. / Tallant, C. / Kiyani, W. / Shrestha, L. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. ...Kopec, J. / Oberholzer, A. / Fitzpatrick, F. / Newman, J. / Tallant, C. / Kiyani, W. / Shrestha, L. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.
CitationJournal: To be Published
Title: Crystal Structure of Human Tryptophane Hydroxylase 2 (Tph2), Catalytic Domain
Authors: Kopec, J. / Oberholzer, A. / Fitzpatrick, F. / Newman, J. / Tallant, C. / Shrestha, L. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.
History
DepositionSep 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...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 / struct_conn / struct_site
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 / _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 2
B: TRYPTOPHAN 5-HYDROXYLASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7536
Polymers80,5032
Non-polymers2504
Water2,000111
1
A: TRYPTOPHAN 5-HYDROXYLASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3773
Polymers40,2521
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRYPTOPHAN 5-HYDROXYLASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3773
Polymers40,2521
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.960, 100.199, 89.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein TRYPTOPHAN 5-HYDROXYLASE 2 / Tryptophan hydroxylase / NEURONAL TRYPTOPHAN HYDROXYLASE / TRYPTOPHAN 5-MONOOXYGENASE 2


Mass: 40251.742 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 148-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: Q8IWU9, tryptophan 5-monooxygenase
#2: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growDetails: 0.20M SODIUM ACETATE; 0.1M BIS-TRIS- PROPANE PH 6.5; 20.0% PEG 3350; 10.0% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.63→44.5 Å / Num. obs: 26141 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 58.83 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.9
Reflection shellResolution: 2.63→2.75 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.32 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PAH

2pah


Resolution: 2.63→44.504 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 1301 5 %
Rwork0.1977 --
obs0.2001 26100 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→44.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 12 111 5335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025354
X-RAY DIFFRACTIONf_angle_d0.5317292
X-RAY DIFFRACTIONf_dihedral_angle_d10.8211849
X-RAY DIFFRACTIONf_chiral_restr0.02810
X-RAY DIFFRACTIONf_plane_restr0.002953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6301-2.73530.33561410.29142703X-RAY DIFFRACTION100
2.7353-2.85980.34321550.26492692X-RAY DIFFRACTION100
2.8598-3.01060.30021560.23952712X-RAY DIFFRACTION100
3.0106-3.19910.2981130.23072762X-RAY DIFFRACTION100
3.1991-3.44610.30981170.22632752X-RAY DIFFRACTION100
3.4461-3.79270.22831420.19562723X-RAY DIFFRACTION100
3.7927-4.34110.21521160.16482819X-RAY DIFFRACTION100
4.3411-5.46770.20921420.17222783X-RAY DIFFRACTION100
5.4677-44.51070.21882190.18652853X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5038-0.5356-0.12340.2580.48260.2919-0.0519-0.110.0549-0.0015-0.0218-0.0842-0.0492-0.1761-0.00010.41040.04820.03220.3080.03460.4217-19.72929.7997-43.1616
20.2434-0.124-0.0580.1610.09140.4366-0.05940.05980.62780.10180.5547-0.7108-0.32690.83790.17960.3964-0.0328-0.00520.7113-0.25520.82053.004133.0733-40.3152
30.4905-0.0133-0.20960.58960.16890.8254-0.0792-0.1940.12590.45050.2063-0.10190.38670.16830.32420.41440.1225-0.00710.459-0.09520.3921-7.789921.6024-39.1259
40.30320.12330.04330.06850.00130.00730.2915-0.3758-0.86130.42730.1923-0.32420.47840.36880.02820.75440.2735-0.30020.6835-0.1950.6391-3.139811.3503-32.2382
50.3186-0.03490.18880.5151-0.08540.15930.1970.36340.0898-0.1412-0.01980.1596-0.0832-0.01530.11890.2758-0.03610.00010.22830.01310.1998-4.23916.8907-62.6839
60.0412-0.0324-0.02080.00970.0057-0.007-0.23650.31380.53380.4771-0.07790.539-0.00430.2194-0.00160.545-0.02150.04670.49550.25460.8515.854731.468-71.8408
70.2232-0.0386-0.26980.0446-0.03370.3223-0.25090.63820.8235-0.1245-0.15170.7473-0.889-1.0133-0.33241.34550.0911-0.41420.79780.44751.0115-14.563337.5279-83.6474
80.5543-0.32330.16420.396-0.20620.285-0.31850.32030.9301-0.47090.09220.0538-0.2222-0.3472-0.18130.5285-0.0292-0.17520.72670.41730.5637-13.137127.6625-78.1602
90.0130.09970.04020.2535-0.01740.0447-0.18620.66340.0858-0.4765-0.0087-0.1194-0.17970.039-0.07860.6194-0.10050.02820.82730.16240.33791.582518.0367-79.1124
100.02370.0023-0.01220.0004-0.01210.00240.37670.2929-0.4012-0.0922-0.32040.2829-0.24850.3353-0.00010.9941-0.1963-0.18371.32050.04350.6492-11.280112.7747-88.065
110.00950.00470.0447-0.0050.00440.06280.08370.1644-0.0101-0.2679-0.14210.06090.0183-0.0968-0.17930.84130.0017-0.45181.46750.5133-0.0627-14.05618.3-94.0834
120.00820.0091-0.00280.10120.05420.01970.03220.8004-0.5461-0.50740.3363-0.33710.32680.174900.81530.0356-0.03110.99830.08340.8911-1.798111.8097-87.1788
130.12780.04370.12890.09520.07180.0580.22970.1894-0.12510.0772-0.0932-0.2119-0.1864-0.141400.3804-0.0186-0.01240.3970.05970.50666.94616.4262-66.0285
140.00150.0385-0.02720.02830.0914-0.00310.3096-0.42660.32780.165-0.15590.1033-0.03690.01880.03570.3905-0.01430.02110.2430.01270.3952-6.04831.8534-55.426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 142 THROUGH 213 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 214 THROUGH 270 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 271 THROUGH 383 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 384 THROUGH 437 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 438 THROUGH 490 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 150 THROUGH 171 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 172 THROUGH 234 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 235 THROUGH 329 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 330 THROUGH 359 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 360 THROUGH 375 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 376 THROUGH 396 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 397 THROUGH 436 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 437 THROUGH 459 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 460 THROUGH 490 )

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