PDB-3qcp: QSOX from Trypanosoma brucei

ID or keywords:

Entry

Database: PDB / ID: 3qcp

Title

QSOX from Trypanosoma brucei

Components

QSOX from Trypanosoma brucei (TbQSOX)

Keywords

OXIDOREDUCTASE / ERV fold / thioredoxin fold / sulfhydryl oxidase

Function / homology

Function and homology information

flavin-dependent sulfhydryl oxidase activity / thiol oxidase / thiol oxidase activity / protein disulfide isomerase activity / protein folding / Golgi membrane / nucleotide binding / extracellular space
Similarity search - Function

Biological species

Trypanosoma brucei (eukaryote)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Alon, A. / Fass, D.

Citation

Journal: Nature / Year: 2012
Title: The dynamic disulphide relay of quiescin sulphydryl oxidase.
Authors: Alon, A. / Grossman, I. / Gat, Y. / Kodali, V.K. / DiMaio, F. / Mehlman, T. / Haran, G. / Baker, D. / Thorpe, C. / Fass, D.

History

Deposition	Jan 17, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 30, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 22, 2012	Group: Database references
Revision 1.2	Aug 29, 2012	Group: Database references
Revision 1.3	Sep 13, 2023	Group: 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 27, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3qcp.cif.gz	105.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3qcp.ent.gz	78.9 KB	Display	PDB format
PDBx/mmJSON format	3qcp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3qcp_validation.pdf.gz	834.7 KB	Display	wwPDB validaton report
Full document	3qcp_full_validation.pdf.gz	843 KB	Display
Data in XML	3qcp_validation.xml.gz	19.6 KB	Display
Data in CIF	3qcp_validation.cif.gz	27.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qc/3qcp ftp://data.pdbj.org/pub/pdb/validation_reports/qc/3qcp	HTTPS FTP

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Related structure data

Related structure data	3q6oC 3qd9C 3t58C 3t59C 3ed3S 3llkS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4krc-d 1d8a-d 1b93-d 5kd7-3 1hh4-1 2pnf-d 2wvo-d 6t62-d 1bjm-d 4b63-d 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	#233 - May 2019 S-Nitrosylated Hemoglobin similarity (3) #91 - Jul 2007 Thymine Dimers similarity (3)

Deposited unit

A: QSOX from Trypanosoma brucei (TbQSOX)

hetero molecules

53 kDa, 1 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)	112.373, 61.399, 74.655
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	QSOX from Trypanosoma brucei (TbQSOX) Mass: 52241.465 Da / Num. of mol.: 1 / Fragment: UNP residues 20-485 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: QSOX, Tb927.6.1850 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: Q585M6, thiol oxidase
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 50.1 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 14-18% w/v polyethylene glycol (PEG) 2K monomethyl ether (MME), 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 9, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. all: 23751 / Num. obs: 23627 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / R_sym value: 0.072 / Net I/σ(I): 10.4
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 1.8 / R_sym value: 0.652 / % possible all: 94.5

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.7_629)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 3LLK and 3ED3

3llk

3ed3

Resolution: 2.3→33.48 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2449	1608	6.82 %	random
R_work	0.1966	-	-	-
obs	-	23564	99.78 %	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 46.686 Å² / k_sol: 0.313 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.3→33.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3251	0	53	185	3489

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3397
X-RAY DIFFRACTION	f_angle_d	1.142	4612
X-RAY DIFFRACTION	f_dihedral_angle_d	15.463	1227
X-RAY DIFFRACTION	f_chiral_restr	0.092	499
X-RAY DIFFRACTION	f_plane_restr	0.006	597

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 (%)
2.3-2.3825	0.3504	155	0.2939	2117	X-RAY DIFFRACTION	98
2.3825-2.4778	0.2937	159	0.237	2170	X-RAY DIFFRACTION	100
2.4778-2.5906	0.273	150	0.227	2159	X-RAY DIFFRACTION	100
2.5906-2.7271	0.3462	153	0.2389	2178	X-RAY DIFFRACTION	100
2.7271-2.8979	0.2911	155	0.2204	2180	X-RAY DIFFRACTION	100
2.8979-3.1215	0.2658	163	0.216	2189	X-RAY DIFFRACTION	100
3.1215-3.4353	0.3074	173	0.2062	2181	X-RAY DIFFRACTION	100
3.4353-3.9317	0.2294	154	0.2011	2211	X-RAY DIFFRACTION	100
3.9317-4.951	0.1924	168	0.153	2236	X-RAY DIFFRACTION	100
4.951-33.4833	0.2131	178	0.181	2335	X-RAY DIFFRACTION	100

Refinement TLS params.

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

ID	L11 (°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)
1	0.8031	-0.7299	0.1739	0.9495	0.0384	0.3893	0.0234	0.0202	-0.1979	0.1453	0.0217	0.396	0.0659	-0.0029	0.017	0.2366	-0.0065	0.0172	0.2712	0.0551	0.3572	34.8993	-31.6709	-4.4382
2	3.134	-1.8233	-0.7407	7.2294	3.0453	1.8471	0.3316	0.6993	-0.1319	-1.0821	-0.3856	0.4214	-0.1732	0.2722	0.0123	0.3344	0.0429	-0.1059	0.3347	0.0273	0.3178	37.3729	-25.1906	-17.6483
3	0.7682	0.0833	0.1627	0.6771	0.6066	0.5485	0.1443	-0.05	-0.3675	0.2311	-0.0902	-0.0608	0.0213	-0.1424	-0.0086	0.2427	-0.0133	0.057	0.1607	0.0359	0.2825	41.658	-30.3186	0.7156
4	2.5531	-1.2691	1.7907	1.7902	-0.4969	1.7789	-0.0962	-0.2111	0.3157	-0.2383	-0.1413	-0.1823	0.0559	-0.2387	0.206	0.217	0.0406	0.0096	0.1979	0.0088	0.1859	36.8447	-17.0942	0.1589
5	2.0529	0.5196	0.1608	0.7347	-0.4547	1.4391	0.1042	0.327	-0.1324	-0.1177	-0.1294	-0.2398	-0.006	0.0523	0.025	0.2573	0.01	0.0546	0.1808	-0.0004	0.3116	46.1917	-28.2139	-7.2905
6	1.353	-0.49	0.6145	0.5358	-0.7624	3.7086	-0.0248	0.2601	0.496	-0.2137	-0.1901	-0.0912	0.4447	-0.0197	0.0675	0.3173	0.0136	0.0232	0.2706	0.1144	0.3131	49.3907	-22.904	-9.7599
7	0.3674	-0.1466	0.2529	0.1769	0.0991	1.0176	-0.104	0.0263	0.309	-0.0837	-0.2343	-0.2783	-0.2457	0.1453	0.095	0.2906	-0.0008	-0.0022	0.1165	0.0254	0.3822	50.2011	-16.4957	-2.218
8	2.6427	0.1972	-0.3692	1.8293	-0.7645	1.1234	0.1449	0.2172	0.1079	0.1263	-0.2658	-0.1908	-0.2793	0.2201	-0.0039	0.3371	0.0519	0.0014	0.3294	0.1761	0.4179	42.2586	-11.0086	-15.6582
9	1.4913	-1.3827	-0.8778	3.0877	-1.0434	4.9107	0.2962	0.1198	-0.1346	0.0647	0.0219	0.2711	-0.3206	-0.7004	-0.2237	0.2694	0.0434	-0.0104	0.2817	0.0737	0.3134	28.0961	-21.9027	-7.8864
10	0.6722	-0.4277	0.4834	0.5311	0.1067	1.0131	0.1079	0.1735	-0.0539	-0.069	-0.3025	0.0799	-0.1088	-0.279	-0.0466	0.2699	0.0563	0.0201	0.367	0.0811	0.3041	23.9882	-10.8028	-20.7103
11	0.0939	0.1111	-0.1038	0.1496	-0.0969	0.2284	-0.0859	0.3077	0.3282	-0.1295	-0.144	-0.1135	-0.1391	0.2118	-0.0831	0.3075	0.1949	-0.1605	0.4974	0.6834	0.5502	27.867	4.5322	-23.6789
12	0.2677	-0.153	0.4984	1.8221	0.321	1.1476	-0.1223	0.0955	0.2064	0.1272	-0.2682	-0.0194	-0.0207	0.1431	0.1325	0.2209	0.0015	-0.0453	0.2043	0.0902	0.2987	28.0034	-2.344	-13.4734
13	1.8241	-0.002	-0.0321	0.7275	0.219	0.1519	0.1769	0.8531	0.0621	-0.1254	-0.0825	0.0278	0.0258	-0.1369	0.0835	0.3175	0.1098	-0.0764	0.4855	-0.0689	0.22	19.3496	-13.4874	-23.3459
14	0.4225	0.4523	0.4276	0.5387	0.278	1.0393	0.0831	0.5568	0.1351	-0.0346	0.0654	0.0273	0.0663	0.2197	0.0558	0.3311	0.1783	-0.0162	1.0257	0.3494	0.3717	29.2485	-7.5328	-33.1479
15	0.4971	0.0541	-0.1006	0.0046	-0.0106	0.0211	0.3122	0.675	0.0817	-0.5493	-0.309	-0.0459	0.7096	0.5369	-0.0506	0.6607	0.2497	-0.1143	1.3424	0.049	0.4113	23.4608	-10.0134	-41.773
16	1.1663	-1.0071	0.3315	2.9113	-0.8716	0.7783	0.2808	0.777	-0.141	-0.8226	-0.0064	0.0176	0.2587	-0.0478	-0.1149	0.554	0.1527	-0.1118	1.2531	-0.207	0.1819	20.3498	-21.0005	-36.5194
17	0.4724	-0.4656	0.315	0.4576	-0.3157	0.2887	0.0556	0.2921	-0.1259	-0.1528	-0.0746	0.0978	-0.068	-0.195	0.0507	0.4143	0.1251	-0.2526	0.6828	-0.4285	0.4675	15.7237	-25.9408	-29.4198
18	1.3882	1.1935	0.3343	1.8714	0.0171	2.0811	0.2349	0.4343	0.0163	-0.503	-0.0727	0.3305	0.6132	0.4245	-0.1399	0.7843	-0.0251	-0.3913	1.3458	-0.1191	0.6194	3.9674	-19.8173	-40.2086
19	1.053	0.5511	0.9473	0.3727	0.4821	1.0705	0.0332	0.2704	0.0258	-0.1451	0.0075	0.1664	0.0677	0.0263	0.1044	0.2615	0.2407	-0.1609	0.9307	-0.0215	0.3925	7.9456	-6.8577	-27.4803
20	5.1972	-1.5906	-0.5166	2.4836	-2.4939	4.5571	-0.5672	0.3456	-0.5797	0.9433	0.4321	-1.2619	-0.0589	0.0148	0.1059	0.4438	0.1556	-0.1244	0.4271	-0.2378	0.7503	9.903	-11.5821	-6.06

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 29:48)
2	X-RAY DIFFRACTION	2	(chain A and resid 49:56)
3	X-RAY DIFFRACTION	3	(chain A and resid 57:76)
4	X-RAY DIFFRACTION	4	(chain A and resid 77:91)
5	X-RAY DIFFRACTION	5	(chain A and resid 92:134)
6	X-RAY DIFFRACTION	6	(chain A and resid 135:154)
7	X-RAY DIFFRACTION	7	(chain A and resid 155:170)
8	X-RAY DIFFRACTION	8	(chain A and resid 171:180)
9	X-RAY DIFFRACTION	9	(chain A and resid 181:197)
10	X-RAY DIFFRACTION	10	(chain A and resid 198:240)
11	X-RAY DIFFRACTION	11	(chain A and resid 241:276)
12	X-RAY DIFFRACTION	12	(chain A and resid 277:297)
13	X-RAY DIFFRACTION	13	(chain A and resid 298:333)
14	X-RAY DIFFRACTION	14	(chain A and resid 334:354)
15	X-RAY DIFFRACTION	15	(chain A and resid 355:369)
16	X-RAY DIFFRACTION	16	(chain A and resid 370:388)
17	X-RAY DIFFRACTION	17	(chain A and resid 389:401)
18	X-RAY DIFFRACTION	18	(chain A and resid 402:420)
19	X-RAY DIFFRACTION	19	(chain A and resid 421:435)
20	X-RAY DIFFRACTION	20	(chain A and resid 436:446)

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