PDB-1zvf: The crystal structure of 3-hydroxyanthranilate 3,4-dioxygenase fr...

ID or keywords:

Entry

Database: PDB / ID: 1zvf

Title

The crystal structure of 3-hydroxyanthranilate 3,4-dioxygenase from Saccharomyces cerevisiae

Components

3-hydroxyanthranilate 3,4-dioxygenase

Keywords

OXIDOREDUCTASE / jellyroll beta-barrel

Function / homology

Function and homology information

quinolinate metabolic process / Tryptophan catabolism / 3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilate 3,4-dioxygenase activity / quinolinate biosynthetic process / anthranilate metabolic process / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / ferrous iron binding / nucleus / cytoplasm
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.41 Å

Authors

Li, X. / Guo, M. / Teng, M. / Niu, L.

Citation

Journal: To be published
Title: The crystal structure of 3-hydroxyanthranilate 3,4-dioxygenase from Saccharomyces cerevisiae
Authors: Li, X. / Guo, M. / Teng, M. / Niu, L.

History

Deposition	Jun 2, 2005	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 2, 2006	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 11, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1zvf.cif.gz	83.1 KB	Display	PDBx/mmCIF format
PDB format	pdb1zvf.ent.gz	62.7 KB	Display	PDB format
PDBx/mmJSON format	1zvf.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	1zvf_validation.pdf.gz	435.7 KB	Display	wwPDB validaton report
Full document	1zvf_full_validation.pdf.gz	443.2 KB	Display
Data in XML	1zvf_validation.xml.gz	15.6 KB	Display
Data in CIF	1zvf_validation.cif.gz	20.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zv/1zvf ftp://data.pdbj.org/pub/pdb/validation_reports/zv/1zvf	HTTPS FTP

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Related structure data

Similar structure data	6x11-1 6vib-1 4hsj-1 6d60-1 6d61-1 6via-1 4l2n-2 1yfx-1 6bvq-1 6cd3-1 Search similar-shape structures by Omokage search (details) 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: 3-hydroxyanthranilate 3,4-dioxygenase

B: 3-hydroxyanthranilate 3,4-dioxygenase

hetero molecules

40.6 kDa, 2 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)	41.104, 66.195, 130.188
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	3-hydroxyanthranilate 3,4-dioxygenase / 3-HAO / 3- hydroxyanthranilic acid dioxygenase / 3-hydroxyanthranilate oxygenase / Biosynthesis of ...3-HAO / 3- hydroxyanthranilic acid dioxygenase / 3-hydroxyanthranilate oxygenase / Biosynthesis of nicotinic acid protein 1 Mass: 20187.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P47096, 3-hydroxyanthranilate 3,4-dioxygenase
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 43.3 %
Crystal grow	Temperature: 293 K / Method: hanging drop / pH: 8.5 Details: 30% PEG4000, 0.2M NaAc, 0.1M Tris_HCl, pH 8.5, hanging drop, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1

Diffraction source

Source:

SYNCHROTRON / Site:

CHESS

/ Beamline: A1 / Wavelength: 0.979, 0.9798, 0.9802, 0.9500

Detector

Detector: CCD

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.979	1
2	0.9798	1
3	0.9802	1
4	0.95	1

Reflection

D res high: 2.4 Å / D res low: 30 Å

Redundancy (%)	ID	Number	R_merge(I) obs	Χ²	% possible obs
12.3	1	13576	0.082	1.044	93.2
12.4	2	13806	0.076	1.003	93.7
12.2	3	13655	0.076	0.974	93

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.49	30	99.3	1	0.065	0.726	11.6
5.16	6.49	99.9	1	0.065	1.018	13.1
4.51	5.16	100	1	0.055	1	13.2
4.1	4.51	99.9	1	0.056	0.986	13.4
3.81	4.1	100	1	0.063	1.079	13.5
3.58	3.81	100	1	0.067	1.097	13.6
3.4	3.58	100	1	0.077	1.054	13.6
3.26	3.4	100	1	0.088	1.066	13.6
3.13	3.26	99.9	1	0.105	1.113	13.4
3.02	3.13	99.7	1	0.128	1.08	13.3
2.93	3.02	99.2	1	0.135	1.08	12.9
2.85	2.93	98.2	1	0.179	1.072	12.5
2.77	2.85	97.5	1	0.175	1.099	12.1
2.7	2.77	91.8	1	0.19	1.024	11.7
2.64	2.7	91.4	1	0.234	1.095	11.2
2.59	2.64	86.1	1	0.246	1.044	10.9
2.53	2.59	81.9	1	0.21	1.08	10
2.49	2.53	76.5	1	0.229	1.072	9.9
2.44	2.49	72.5	1	0.222	1.073	9.8
2.4	2.44	67.9	1	0.244	1.111	9.2
6.49	30	99.3	2	0.056	0.618	11.7
5.16	6.49	100	2	0.055	0.99	13.2
4.51	5.16	100	2	0.049	1.053	13.4
4.1	4.51	99.9	2	0.052	1.001	13.5
3.81	4.1	100	2	0.06	1.05	13.7
3.58	3.81	100	2	0.065	1.025	13.7
3.4	3.58	100	2	0.074	1.009	13.7
3.26	3.4	100	2	0.088	1.027	13.8
3.13	3.26	99.9	2	0.101	1.027	13.5
3.02	3.13	99.7	2	0.126	1.046	13.4
2.93	3.02	99.9	2	0.143	0.964	12.9
2.85	2.93	98	2	0.177	1.028	12.6
2.77	2.85	96.6	2	0.186	1.049	12.5
2.7	2.77	93.2	2	0.202	1.02	11.9
2.64	2.7	92.6	2	0.265	1.108	11.2
2.59	2.64	88.4	2	0.256	0.999	10.9
2.53	2.59	84	2	0.239	1.051	10.2
2.49	2.53	78.5	2	0.234	0.999	9.8
2.44	2.49	73	2	0.235	1.048	9.7
2.4	2.44	67.6	2	0.283	1.032	9.2
6.49	30	99.4	3	0.053	0.446	11.6
5.16	6.49	100	3	0.054	1.069	13.1
4.51	5.16	100	3	0.049	1.009	13.3
4.1	4.51	99.9	3	0.052	0.997	13.4
3.81	4.1	100	3	0.059	1.032	13.5
3.58	3.81	100	3	0.065	1.009	13.6
3.4	3.58	100	3	0.075	0.998	13.5
3.26	3.4	100	3	0.085	0.975	13.5
3.13	3.26	99.9	3	0.1	1.006	13.4
3.02	3.13	99.7	3	0.123	1.006	13.1
2.93	3.02	99.3	3	0.139	0.939	12.7
2.85	2.93	97.7	3	0.177	1.042	12.4
2.77	2.85	96.1	3	0.178	1.021	12.2
2.7	2.77	92	3	0.193	1.008	11.6
2.64	2.7	89.7	3	0.242	0.997	11.2
2.59	2.64	85.9	3	0.252	0.976	10.8
2.53	2.59	81.9	3	0.239	1.025	10.1
2.49	2.53	74.9	3	0.222	1.033	9.8
2.44	2.49	74.6	3	0.233	0.98	9.4
2.4	2.44	66.9	3	0.273	0.955	8.9

Reflection

Resolution: 2.4→30 Å / Num. obs: 13576 / % possible obs: 93.2 % / Redundancy: 12.3 % / R_merge(I) obs: 0.082 / Χ²: 1.044

Reflection shell

Resolution (Å)	% possible obs (%)	Redundancy (%)	R_merge(I) obs	Num. measured obs	Χ²
2.4-2.44	67.9	9.2	0.244	489	1.111
2.44-2.49	72.5	9.8	0.222	496	1.073
2.49-2.53	76.5	9.9	0.229	556	1.072
2.53-2.59	81.9	10	0.21	582	1.08
2.59-2.64	86.1	10.9	0.246	603	1.044
2.64-2.7	91.4	11.2	0.234	663	1.095
2.7-2.77	91.8	11.7	0.19	660	1.024
2.77-2.85	97.5	12.1	0.175	676	1.099
2.85-2.93	98.2	12.5	0.179	724	1.072
2.93-3.02	99.2	12.9	0.135	708	1.08
3.02-3.13	99.7	13.3	0.128	720	1.08
3.13-3.26	99.9	13.4	0.105	715	1.113
3.26-3.4	100	13.6	0.088	733	1.066
3.4-3.58	100	13.6	0.077	707	1.054
3.58-3.81	100	13.6	0.067	740	1.097
3.81-4.1	100	13.5	0.063	742	1.079
4.1-4.51	99.9	13.4	0.056	732	0.986
4.51-5.16	100	13.2	0.055	757	1
5.16-6.49	99.9	13.1	0.065	748	1.018
6.49-30	99.3	11.6	0.065	825	0.726

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	1.601	data extraction
HKL-2000		data reduction
SHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.41→20 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.909 / SU B: 20.444 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.939 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2675	976	7.3 %	RANDOM
R_work	0.21672	-	-	-
all	0.223	-	-	-
obs	0.2203	12470	93.42 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 47.372 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.43 Å²	0 Å²	0 Å²
2-	-	9.9 Å²	0 Å²
3-	-	-	-5.47 Å²

Refinement step

Cycle: LAST / Resolution: 2.41→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2810	0	4	60	2874

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	2882
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.31	1.953	3914
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.263	5	348
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.572	25.139	144
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.292	15	496
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.812	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	421
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2223
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	1227
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	1862
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.2	162
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.247	0.2	40
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.137	0.2	2
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.154	1.5	1788
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.808	2	2847
X-RAY DIFFRACTION	r_scbond_it	1.535	3	1235
X-RAY DIFFRACTION	r_scangle_it	2.36	4.5	1067
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.406→2.534 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.301	106	-
R_work	0.279	1368	-
obs	-	-	72.58 %

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