PDB-2pes: Urate Oxidase in complex with tris-dipicolinate Lutetium

ID or keywords:

Entry

Database: PDB / ID: 2pes

Title

Urate Oxidase in complex with tris-dipicolinate Lutetium

Components

Uricase

Keywords

OXIDOREDUCTASE / URATE OXIDASE TRIS-DIPICOLINATE LUTETIUM 8-AZAXANTHIN X-RAY

Function / homology

Function and homology information

purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome
Similarity search - Function

Biological species

Aspergillus flavus (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.6 Å

Authors

Pompidor, G. / Vicat, J. / Kahn, R.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: A dipicolinate lanthanide complex for solving protein structures using anomalous diffraction.
Authors: Pompidor, G. / Maury, O. / Vicat, J. / Kahn, R.

History

Deposition	Apr 3, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 22, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.2	Mar 21, 2012	Group: Database references
Revision 1.3	Feb 21, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _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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Download

PDBx/mmCIF format	2pes.cif.gz	83 KB	Display	PDBx/mmCIF format
PDB format	pdb2pes.ent.gz	60.2 KB	Display	PDB format
PDBx/mmJSON format	2pes.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2pes_validation.pdf.gz	454.5 KB	Display	wwPDB validaton report
Full document	2pes_full_validation.pdf.gz	457.9 KB	Display
Data in XML	2pes_validation.xml.gz	15.8 KB	Display
Data in CIF	2pes_validation.cif.gz	23.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pe/2pes ftp://data.pdbj.org/pub/pdb/validation_reports/pe/2pes	HTTPS FTP

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Related structure data

Related structure data	2pe7C 3lgrC 1r51 2pc2 C: citing same article (ref.)
Similar structure data	4op9-d 3p9o-d 3plj-d 2icq-d 3pkf-d 2fxl-d 3pkh-d 6ia3-d 3pjk-d 6ia1-d Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#117 - Sep 2009 Xanthine Oxidoreductase similarity (6) #143 - Nov 2011 Toll-like Receptors similarity (1)

Deposited unit

A: Uricase

hetero molecules

35.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

A: Uricase

hetero molecules

A: Uricase

hetero molecules

A: Uricase

hetero molecules

A: Uricase

hetero molecules

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

Unit cell

Length a, b, c (Å)	79.550, 95.320, 104.330
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

#1: Protein	Uricase / Urate oxidase Mass: 33498.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus flavus (mold) References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical	ChemComp-LU / LUTETIUM (III) ION / LU Mass: 174.967 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Lu
#3: Chemical	ChemComp-AZA / 8-AZAXANTHINE Mass: 153.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₃N₅O₂
#4: Chemical	ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID Mass: 167.119 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₇H₅NO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H₂O
Nonpolymer details	ACCORDING TO AUTHORS THE LIGAND PDC IS IN THE BASIC (DEPROTONATED) FORM (C7H3N1O4)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.95 Å³/Da / Density % sol: 58.32 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 5% PEG 8000, 0.1 Tris, pH 8.5, VAPOR DIFFUSION, 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:

ESRF

/ Beamline: BM30A / Wavelength: 0.979700, 1.341332

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 20, 2006

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9797	1
2	1.341332	1

Reflection

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	R_sym value	D res high (Å)	D res low (Å)	Num. obs	% possible obs
6.6	1	4.7	391421	0.066	0.066	1.518	47.673	59288	96.6
6.4	2	11.8	148449	0.041	0.041	2.07	47.298	23324	97.1
6.7	3	9.5	157773	0.043	0.043	2.079	47.727	23722	97.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
4.8	47.67	78.7	1	0.036	0.036	5.6
3.39	4.8	92.3	1	0.037	0.037	6.3
2.77	3.39	99.9	1	0.035	0.035	7.2
2.4	2.77	100	1	0.042	0.042	7.3
2.15	2.4	100	1	0.051	0.051	7.3
1.96	2.15	100	1	0.069	0.069	7.4
1.81	1.96	100	1	0.115	0.115	7.4
1.7	1.81	100	1	0.196	0.196	7.3
1.6	1.7	99.9	1	0.399	0.399	6.8
1.52	1.6	84.6	1	1.084	1.084	3.1
6.55	47.3	80.9	2	0.033	0.033	5.5
4.63	6.55	95.9	2	0.033	0.033	6.4
3.78	4.63	97.2	2	0.031	0.031	6.5
3.27	3.78	99.6	2	0.031	0.031	6.9
2.93	3.27	100	2	0.035	0.035	7
2.67	2.93	100	2	0.038	0.038	7.1
2.47	2.67	100	2	0.044	0.044	7.1
2.31	2.47	100	2	0.048	0.048	7.1
2.18	2.31	100	2	0.067	0.067	6.6
2.07	2.18	87.4	2	0.306	0.306	3.1
6.58	47.73	99.7	3	0.023	0.023	6.4
4.65	6.58	100	3	0.027	0.027	7.1
3.8	4.65	100	3	0.024	0.024	7.2
3.29	3.8	100	3	0.026	0.026	7.3
2.94	3.29	100	3	0.036	0.036	7.3
2.68	2.94	100	3	0.053	0.053	7.3
2.49	2.68	100	3	0.08	0.08	7.3
2.32	2.49	100	3	0.112	0.112	7.3
2.19	2.32	100	3	0.158	0.158	6.8
2.08	2.19	85.1	3	0.683	0.683	3.1

Reflection

Resolution: 1.518→47.673 Å / Num. obs: 59288 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / B_iso Wilson estimate: 18 Å² / R_merge(I) obs: 0.066 / R_sym value: 0.066 / Net I/σ(I): 4.7

Reflection shell

R_merge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.52-1.6	3.1	0.4	22936	7489	1.084	84.6
1.6-1.7	6.8	0.6	56847	8420	0.399	99.9
1.7-1.81	7.3	3.8	57957	7890	0.196	100
1.81-1.96	7.4	6.5	54370	7381	0.115	100
1.96-2.15	7.4	10.7	50220	6819	0.069	100
2.15-2.4	7.3	14	45194	6172	0.051	100
2.4-2.77	7.3	16.1	40080	5477	0.042	100
2.77-3.39	7.2	17.9	33519	4652	0.035	99.9
3.39-4.8	6.3	18.4	21221	3361	0.037	92.3
4.8-47.67	5.6	17.5	9077	1627	0.036	78.7

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Phasing

Phasing

Method:

MAD

Phasing MAD set

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Lowest resolution (Å)	Reflection acentric	Reflection centric
ISO_1	0	0	1.7	47.72	39363	2922
ISO_2	0.987	1.004	1.7	47.72	20035	1762
ISO_3	0.996	0.996	1.7	47.72	20063	1759
ANO_1	0.74	0	1.7	47.72	39122	0
ANO_2	0.6	0	1.7	47.72	20048	0
ANO_3	0.483	0	1.7	47.72	19949	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Reflection acentric	Reflection centric
ISO_1	7.51-47.72	0	0	176	72
ISO_1	5.35-7.51	0	0	699	136
ISO_1	4.37-5.35	0	0	849	140
ISO_1	3.79-4.37	0	0	1126	148
ISO_1	3.39-3.79	0	0	1341	138
ISO_1	3.1-3.39	0	0	1519	138
ISO_1	2.87-3.1	0	0	1716	149
ISO_1	2.69-2.87	0	0	1829	140
ISO_1	2.53-2.69	0	0	1946	135
ISO_1	2.4-2.53	0	0	2082	151
ISO_1	2.29-2.4	0	0	2199	146
ISO_1	2.19-2.29	0	0	2264	131
ISO_1	2.11-2.19	0	0	2239	152
ISO_1	2.03-2.11	0	0	2462	153
ISO_1	1.96-2.03	0	0	2615	155
ISO_1	1.9-1.96	0	0	2670	165
ISO_1	1.84-1.9	0	0	2786	167
ISO_1	1.79-1.84	0	0	2873	171
ISO_1	1.74-1.79	0	0	2943	171
ISO_1	1.7-1.74	0	0	3029	164
ANO_1	7.51-47.72	0.495	0	145	0
ANO_1	5.35-7.51	0.41	0	658	0
ANO_1	4.37-5.35	0.514	0	757	0
ANO_1	3.79-4.37	0.558	0	1056	0
ANO_1	3.39-3.79	0.631	0	1334	0
ANO_1	3.1-3.39	0.565	0	1519	0
ANO_1	2.87-3.1	0.531	0	1716	0
ANO_1	2.69-2.87	0.558	0	1829	0
ANO_1	2.53-2.69	0.632	0	1946	0
ANO_1	2.4-2.53	0.675	0	2082	0
ANO_1	2.29-2.4	0.751	0	2199	0
ANO_1	2.19-2.29	0.768	0	2264	0
ANO_1	2.11-2.19	0.815	0	2239	0
ANO_1	2.03-2.11	0.87	0	2462	0
ANO_1	1.96-2.03	0.911	0	2615	0
ANO_1	1.9-1.96	0.937	0	2670	0
ANO_1	1.84-1.9	0.955	0	2786	0
ANO_1	1.79-1.84	0.968	0	2873	0
ANO_1	1.74-1.79	0.979	0	2943	0
ANO_1	1.7-1.74	0.984	0	3029	0
ISO_2	7.51-47.72	0.871	0.883	176	72
ISO_2	5.35-7.51	1.01	1.006	699	136
ISO_2	4.37-5.35	1.132	1.123	849	140
ISO_2	3.79-4.37	1.118	1.099	1126	148
ISO_2	3.39-3.79	1.217	1.163	1341	138
ISO_2	3.1-3.39	1.175	1.068	1519	138
ISO_2	2.87-3.1	0.977	1.043	1716	149
ISO_2	2.69-2.87	0.846	0.932	1829	140
ISO_2	2.53-2.69	0.792	0.883	1946	135
ISO_2	2.4-2.53	0.789	0.849	2082	151
ISO_2	2.29-2.4	0.798	0.846	2199	146
ISO_2	2.19-2.29	0.81	0.837	2264	131
ISO_2	2.11-2.19	0.892	0.903	2003	126
ISO_2	2.03-2.11	1.022	1.026	286	12
ISO_2	1.96-2.03	0	0	0	0
ISO_2	1.9-1.96	0	0	0	0
ISO_2	1.84-1.9	0	0	0	0
ISO_2	1.79-1.84	0	0	0	0
ISO_2	1.74-1.79	0	0	0	0
ISO_2	1.7-1.74	0	0	0	0
ANO_2	7.51-47.72	0.301	0	252	0
ANO_2	5.35-7.51	0.289	0	747	0
ANO_2	4.37-5.35	0.31	0	970	0
ANO_2	3.79-4.37	0.314	0	1187	0
ANO_2	3.39-3.79	0.34	0	1347	0
ANO_2	3.1-3.39	0.389	0	1519	0
ANO_2	2.87-3.1	0.428	0	1716	0
ANO_2	2.69-2.87	0.524	0	1829	0
ANO_2	2.53-2.69	0.6	0	1946	0
ANO_2	2.4-2.53	0.695	0	2082	0
ANO_2	2.29-2.4	0.761	0	2199	0
ANO_2	2.19-2.29	0.828	0	2264	0
ANO_2	2.11-2.19	0.946	0	1827	0
ANO_2	2.03-2.11	0.983	0	163	0
ANO_2	1.96-2.03	0	0	0	0
ANO_2	1.9-1.96	0	0	0	0
ANO_2	1.84-1.9	0	0	0	0
ANO_2	1.79-1.84	0	0	0	0
ANO_2	1.74-1.79	0	0	0	0
ANO_2	1.7-1.74	0	0	0	0
ISO_3	7.51-47.72	1.161	1.013	176	72
ISO_3	5.35-7.51	1.016	1.013	699	136
ISO_3	4.37-5.35	0.985	0.992	849	140
ISO_3	3.79-4.37	0.957	0.979	1126	148
ISO_3	3.39-3.79	0.99	0.997	1341	138
ISO_3	3.1-3.39	1.003	1.002	1519	138
ISO_3	2.87-3.1	1.01	1	1716	149
ISO_3	2.69-2.87	1.018	1.025	1829	140
ISO_3	2.53-2.69	1.024	1.001	1946	135
ISO_3	2.4-2.53	1.014	1.016	2082	151
ISO_3	2.29-2.4	0.994	1.024	2199	146
ISO_3	2.19-2.29	0.942	0.961	2264	131
ISO_3	2.11-2.19	0.959	0.963	2083	128
ISO_3	2.03-2.11	0.979	0.986	234	7
ISO_3	1.96-2.03	0	0	0	0
ISO_3	1.9-1.96	0	0	0	0
ISO_3	1.84-1.9	0	0	0	0
ISO_3	1.79-1.84	0	0	0	0
ISO_3	1.74-1.79	0	0	0	0
ISO_3	1.7-1.74	0	0	0	0
ANO_3	7.51-47.72	0.33	0	223	0
ANO_3	5.35-7.51	0.341	0	743	0
ANO_3	4.37-5.35	0.339	0	942	0
ANO_3	3.79-4.37	0.359	0	1179	0
ANO_3	3.39-3.79	0.384	0	1347	0
ANO_3	3.1-3.39	0.384	0	1519	0
ANO_3	2.87-3.1	0.369	0	1716	0
ANO_3	2.69-2.87	0.395	0	1829	0
ANO_3	2.53-2.69	0.422	0	1946	0
ANO_3	2.4-2.53	0.454	0	2082	0
ANO_3	2.29-2.4	0.483	0	2199	0
ANO_3	2.19-2.29	0.537	0	2263	0
ANO_3	2.11-2.19	0.831	0	1829	0
ANO_3	2.03-2.11	0.971	0	132	0
ANO_3	1.96-2.03	0	0	0	0
ANO_3	1.9-1.96	0	0	0	0
ANO_3	1.84-1.9	0	0	0	0
ANO_3	1.79-1.84	0	0	0	0
ANO_3	1.74-1.79	0	0	0	0
ANO_3	1.7-1.74	0	0	0	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	31.041	8.63	26.194	LU	33.18	0.79
2	35.581	8.745	34.172	LU	31.77	0.57
3	1.816	15.168	68.8	LU	46.89	0.41

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 58902

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.84-100	65.3	0.704	514
5.7-7.84	56.1	0.871	761
4.7-5.7	56.7	0.9	955
4.09-4.7	51.2	0.934	1117
3.67-4.09	51.2	0.919	1238
3.35-3.67	54.2	0.929	1376
3.11-3.35	53.8	0.917	1479
2.91-3.11	54.1	0.926	1573
2.75-2.91	52.2	0.924	1690
2.61-2.75	51.9	0.922	1759
2.49-2.61	52.4	0.917	1851
2.38-2.49	52.3	0.924	1916
2.29-2.38	53.7	0.922	2034
2.21-2.29	56.1	0.935	2086
2.13-2.21	59.7	0.924	2139
2.07-2.13	69	0.924	2264
2-2.07	70.6	0.915	2300
1.95-2	71.3	0.911	2347
1.9-1.95	73.2	0.905	2426
1.85-1.9	74	0.897	2493
1.8-1.85	74.8	0.884	2550
1.76-1.8	76.4	0.884	2602
1.72-1.76	77.8	0.881	2665
1.69-1.72	80.4	0.864	2720
1.65-1.69	80.4	0.853	2778
1.62-1.65	83.5	0.832	2839
1.59-1.62	84.4	0.786	2865
1.56-1.59	86.5	0.733	2675
1.53-1.56	87.2	0.55	2890

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Processing

Software

Name	Version	Classification
SCALA		data scaling
SHARP		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction

Refinement

Method to determine structure:

MAD / Resolution: 1.6→15 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.952 / SU B: 1.33 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.195	2605	5 %	RANDOM
R_work	0.179	-	-	-
obs	0.18	51652	98.42 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 18.887 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.04 Å²	0 Å²	0 Å²
2-	-	-0.48 Å²	0 Å²
3-	-	-	-0.57 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2360	0	86	234	2680

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	2531
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	2171
X-RAY DIFFRACTION	r_angle_refined_deg	1.358	1.964	3441
X-RAY DIFFRACTION	r_angle_other_deg	0.809	3	5071
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.93	5	303
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.7	24.522	115
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.297	15	426
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.793	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	373
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2830
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	509
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	414
X-RAY DIFFRACTION	r_nbd_other	0.2	0.2	2012
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1228
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	1287
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	156
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.153	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.082	0.2	19
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.177	0.2	88
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.14	0.2	28
X-RAY DIFFRACTION	r_mcbond_it	1.783	1.5	1940
X-RAY DIFFRACTION	r_mcbond_other	0.213	1.5	605
X-RAY DIFFRACTION	r_mcangle_it	1.664	2	2429
X-RAY DIFFRACTION	r_scbond_it	2.733	3	1261
X-RAY DIFFRACTION	r_scangle_it	3.936	4.5	1009
X-RAY DIFFRACTION	r_sphericity_free	11.897	3	3

LS refinement shell

Resolution: 1.6→1.641 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	170	-
R_work	0.22	3625	-
obs	-	3795	99.71 %

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