PDB-7ui3: Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding

ID or keywords:

Entry

Database: PDB / ID: 7ui3

Title

Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding

Components

Tryptophan 2,3-dioxygenase

Keywords

OXIDOREDUCTASE /

Tryptophan 2 / 3-Dioxygenase / apo-form /

NADH /

OXYGEN BINDING

Function / homology

Function and homology information

response to nitroglycerin / tryptophan catabolic process to acetyl-CoA /

tryptophan 2,3-dioxygenase /

tryptophan 2,3-dioxygenase activity / tryptophan catabolic process to kynurenine / Tryptophan catabolism /

amino acid binding /

oxygen binding / protein homotetramerization /

heme binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.18 Å

Authors

Yeh, S.-R. / Geeraerts, Z.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01 GM115773	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01 GM126297	United States

Citation

Journal: To Be Published
Title: Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding
Authors: Yeh, S.-R. / Geeraerts, Z.

History

Deposition	Mar 28, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 21, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ui3.cif.gz	447.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7ui3.ent.gz	355 KB	Display	PDB format
PDBx/mmJSON format	7ui3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ui/7ui3 ftp://data.pdbj.org/pub/pdb/validation_reports/ui/7ui3	HTTPS FTP

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Related structure data

Related structure data	6pyzS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tryptophan 2,3-dioxygenase

B: Tryptophan 2,3-dioxygenase

C: Tryptophan 2,3-dioxygenase

D: Tryptophan 2,3-dioxygenase

hetero molecules

182 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	143.855, 156.264, 88.986
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Tryptophan 2,3-dioxygenase / / TDO / Tryptamin 2 / 3-dioxygenase / Tryptophan oxygenase / TRPO / Tryptophan pyrrolase / Tryptophanase Mass: 45182.535 Da / Num. of mol.: 4 / Fragment: UNP residues 18-389 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TDO2, TDO / Production host: Escherichia coli (E. coli) / References: UniProt: P48775, tryptophan 2,3-dioxygenase
#2: Chemical	ChemComp-ZIQ / alpha-methyl-L-tryptophan Type: L-peptide linking / Mass: 218.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₁₄N₂O₂
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.55 %
Crystal grow	Temperature: 293 K / Method: microbatch / pH: 5.6 Details: 50 mM Sodium Citrate, pH 5.6 2% Tacsimate PEG 3350 (4-12%)

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 1.54975 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2021
Details: Rh coated flat bent M0, toroidal focusing post-monochromator M1

Radiation

Monochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.54975 Å / Relative weight: 1

Reflection

Resolution: 3.18→19.974 Å / Num. obs: 34269 / % possible obs: 99.5 % / Redundancy: 12.9 % / CC_1/2: 1 / R_merge(I) obs: 0.098 / R_pim(I) all: 0.04 / R_rim(I) all: 0.106 / Net I/σ(I): 18.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
10.55-19.97	13.2	0.032	893	1	0.012	0.034
3.18-3.34	13.8	2.888	4497	0.644	1.163	3.115

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
REFMAC	5.8.0267	refinement
Coot		model building
Aimless		data scaling
PHASER		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6PYZ

6pyz

Resolution: 3.18→19.974 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.934 / WR_factor R_free: 0.26 / WR_factor R_work: 0.227 / SU B: 28.651 / SU ML: 0.452 / Average fsc free: 0.8269 / Average fsc work: 0.8441 / Cross valid method: FREE R-VALUE / ESU R Free: 0.479
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2783	1774	5.191 %
R_work	0.2441	32399	-
all	0.246	-	-
obs	-	34173	99.199 %

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 106.154 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.274 Å²	0 Å²	0 Å²
2-	-	-0.966 Å²	0 Å²
3-	-	-	-3.308 Å²

Refinement step

Cycle: LAST / Resolution: 3.18→19.974 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9040	0	64	0	9104

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	9295
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8097
X-RAY DIFFRACTION	r_angle_refined_deg	1.276	1.633	12634
X-RAY DIFFRACTION	r_angle_other_deg	1.24	1.578	18356
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.737	5	1190
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.81	22.5	464
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.577	15	1349
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.111	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.05	0.2	1239
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	10812
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2242
X-RAY DIFFRACTION	r_nbd_refined	0.242	0.2	2543
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	8137
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	4646
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	4251
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	245
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.195	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.302	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	4.702	12.555	4811
X-RAY DIFFRACTION	r_mcbond_other	4.702	12.554	4810
X-RAY DIFFRACTION	r_mcangle_it	7.57	18.818	5984
X-RAY DIFFRACTION	r_mcangle_other	7.57	18.819	5985
X-RAY DIFFRACTION	r_scbond_it	4.457	12.353	4484
X-RAY DIFFRACTION	r_scbond_other	4.455	12.352	4483
X-RAY DIFFRACTION	r_scangle_it	7.336	18.473	6650
X-RAY DIFFRACTION	r_scangle_other	7.335	18.473	6651
X-RAY DIFFRACTION	r_lrange_it	13.605	230.64	39228
X-RAY DIFFRACTION	r_lrange_other	13.605	230.636	39229
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.129	0.05	8569
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.124	0.05	8152
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.122	0.05	8258
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.111	0.05	8250
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.136	0.05	8448
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.119	0.05	8003

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.18-3.263	0.433	126	0.36	2375	X-RAY DIFFRACTION	99.8802
3.263-3.352	0.409	121	0.346	2292	X-RAY DIFFRACTION	99.7932
3.352-3.449	0.359	133	0.328	2255	X-RAY DIFFRACTION	99.7494
3.449-3.555	0.347	114	0.32	2208	X-RAY DIFFRACTION	99.7851
3.555-3.672	0.357	121	0.324	2107	X-RAY DIFFRACTION	99.8655
3.672-3.801	0.339	101	0.29	2064	X-RAY DIFFRACTION	99.586
3.801-3.944	0.308	113	0.27	1978	X-RAY DIFFRACTION	99.5714
3.944-4.105	0.306	105	0.258	1915	X-RAY DIFFRACTION	99.3117
4.105-4.287	0.305	106	0.251	1813	X-RAY DIFFRACTION	99.1731
4.287-4.496	0.25	104	0.241	1764	X-RAY DIFFRACTION	99.3617
4.496-4.739	0.266	90	0.206	1680	X-RAY DIFFRACTION	99.8308
4.739-5.027	0.241	94	0.199	1582	X-RAY DIFFRACTION	100
5.027-5.373	0.29	54	0.222	1531	X-RAY DIFFRACTION	100
5.373-5.803	0.285	69	0.243	1425	X-RAY DIFFRACTION	99.9331
5.803-6.356	0.355	51	0.285	1318	X-RAY DIFFRACTION	99.5636
6.356-7.105	0.317	84	0.268	1167	X-RAY DIFFRACTION	99.6813
7.105-8.201	0.264	67	0.238	1054	X-RAY DIFFRACTION	99.7331
8.201-10.038	0.194	76	0.193	879	X-RAY DIFFRACTION	99.8954
10.038-14.166	0.187	32	0.167	723	X-RAY DIFFRACTION	100
14.166-19.974	0.267	13	0.261	269	X-RAY DIFFRACTION	61.5721

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