PDB-2q0x: Alpha/Beta hydrolase fold protein of unknown function

ID or keywords:

Entry

Database: PDB / ID: 2q0x

Title

Alpha/Beta hydrolase fold protein of unknown function

Components

Uncharacterized protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha/beta hydrolase fold / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / PSI / Protein Structure Initiative

Function / homology

Fusarinine C esterase SidJ / Protein of unknown function (DUF1749) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Paraflagellar rod component

Function and homology information

Biological species

Trypanosoma brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD /

MAD / Resolution: 2.2 Å

Authors

Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of a Trypanosoma brucei alpha/beta-hydrolase fold protein with unknown function.
Authors: Merritt, E.A. / Holmes, M. / Buckner, F.S. / Van Voorhis, W.C. / Quartly, E. / Phizicky, E.M. / Lauricella, A. / Luft, J. / DeTitta, G. / Neely, H. / Zucker, F. / Hol, W.G.

History

Deposition	May 22, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 26, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.4	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 / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2q0x.cif.gz	128.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2q0x.ent.gz	99.8 KB	Display	PDB format
PDBx/mmJSON format	2q0x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2q0x_validation.pdf.gz	450.4 KB	Display	wwPDB validaton report
Full document	2q0x_full_validation.pdf.gz	456 KB	Display
Data in XML	2q0x_validation.xml.gz	23.5 KB	Display
Data in CIF	2q0x_validation.cif.gz	32.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q0/2q0x ftp://data.pdbj.org/pub/pdb/validation_reports/q0/2q0x	HTTPS FTP

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Related structure data

Similar structure data	4qcb-d 3efb-1 6md6-d 3usz-d 6jg7-d 3wlr-d 7kp0-d 6tr4-2 6jgc-d 4i1i-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: Tbru020260AAA

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

74.9 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)	63.556, 63.556, 303.186
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Uncharacterized protein / Protein DUF1749 Mass: 37359.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: TREU927, 927/4 GUTat10.1 / Gene: Tb10.6k15.0140 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q389W3
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.36 Å³/Da / Density % sol: 39.9 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.4 ul protein: 10.5 mg/ml, 0.4 ul crystallization buffer: 35% PEG 400, 100 mM NaCl, 100 mM MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97953 Å

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 22, 2005 / Details: mirrors

Radiation

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

Radiation wavelength

Wavelength: 0.97953 Å / Relative weight: 1

Refln sys abs

Reflection

Resolution: 2.2→101.062 Å / Num. obs: 37476 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 7.1 % / B_iso Wilson estimate: 49.23797 Å² / R_merge(I) obs: 0.06 / R_sym value: 0.06 / Net I/σ(I): 8.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.2-2.32	6.2	0.612	1.2	33058	5299	0.612	99.5
2.32-2.46	7.3	0.406	1.8	37293	5078	0.406	100
2.46-2.63	7.3	0.262	2.8	35257	4826	0.262	100
2.63-2.84	7.3	0.169	4.4	32553	4444	0.169	100
2.84-3.11	7.3	0.104	6.8	30242	4151	0.104	100
3.11-3.48	7.3	0.067	9.5	27435	3774	0.067	100
3.48-4.02	7.2	0.044	13.2	24248	3363	0.044	100
4.02-4.92	7.1	0.039	14.5	20437	2870	0.039	100
4.92-6.96	6.9	0.037	14.9	15953	2303	0.037	100
6.96-303.19	6.1	0.031	15.5	8286	1368	0.031	99.6

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
TRUNCATE	CCP4_5.0	data reduction
SCALA		data scaling
PDB_EXTRACT	2	data extraction
MAR345	CCD	data collection
MOSFLM		data reduction
SOLVE		phasing
REFMAC	5.2.0019	refinement

Refinement

Method to determine structure:

SAD / Resolution: 2.2→101.02 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.939 / SU B: 12.554 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25	1866	5 %	RANDOM
R_work	0.206	-	-	-
obs	0.208	37326	99.76 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 30.269 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.63 Å²	0.31 Å²	0 Å²
2-	-	0.63 Å²	0 Å²
3-	-	-	-0.94 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→101.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4533	0	12	123	4668

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	4654
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3077
X-RAY DIFFRACTION	r_angle_refined_deg	1.247	1.96	6332
X-RAY DIFFRACTION	r_angle_other_deg	0.915	3	7508
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.264	5	589
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.024	24.093	215
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.936	15	743
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.397	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	717
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	5240
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	932
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	951
X-RAY DIFFRACTION	r_nbd_other	0.196	0.2	3270
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	2259
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	2427
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.18	0.2	191
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.185	0.2	12
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.364	0.2	34
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.131	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	0.374	2	3026
X-RAY DIFFRACTION	r_mcbond_other	0.053	2	1184
X-RAY DIFFRACTION	r_mcangle_it	0.642	3	4722
X-RAY DIFFRACTION	r_scbond_it	0.752	4	1840
X-RAY DIFFRACTION	r_scangle_it	1.145	6	1608

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.343	129	-
R_work	0.285	2516	-
obs	-	2645	98.55 %

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	6.2167	0.3021	-1.7621	8.7346	2.7775	10.2389	0.0455	-0.1442	-0.4972	0.4732	-0.2718	0.286	0.7694	-0.5467	0.2263	0.1621	-0.0397	0.1247	0.1288	0.0867	-0.0052	44.999	20.379	123.545
2	3.2853	-0.4873	-1.9535	3.7187	-0.045	4.4481	0.0997	0.1171	0.0107	0.0747	-0.0254	0.2263	0.051	-0.3018	-0.0743	0.143	-0.0128	0.0305	0.1061	-0.0003	-0.0186	51.05	23.799	117.714
3	5.023	-0.5642	-1.0056	0.9531	-0.5109	3.2691	0.022	0.2496	-0.1059	-0.0338	-0.0538	-0.0337	0.0292	0.0231	0.0318	0.1308	0.0014	0.0106	0.1009	0.0117	-0.0344	62.075	23.033	111.218
4	4.4449	3.2927	-1.7537	4.5668	-1.5905	1.8333	-0.3152	-0.3722	-0.9214	-0.1694	-0.2998	-0.6186	0.6381	0.7452	0.615	0.1167	0.1595	0.1291	0.1084	0.101	0.0432	70.856	9.379	116.925
5	4.9257	-1.1683	0.0608	2.8457	-0.6574	5.9084	0.1868	-0.2319	0.0446	0.1036	-0.2201	-0.4156	0.1633	1.0108	0.0333	0.0366	-0.0434	0.0318	0.2217	0.0655	-0.0491	73.619	25.567	111.12
6	4.9528	-1.1621	-0.8949	2.3052	0.123	4.4392	0.3746	-0.0525	0.5214	0.0405	-0.0818	-0.0331	-0.5689	0.4706	-0.2928	0.1559	-0.1437	0.0966	0.0831	-0.0408	0.0056	67.67	33.04	114.747
7	7.6197	-0.5579	2.9946	8.509	-3.1471	15.4013	0.333	-0.1561	0.0387	0.3737	-0.3774	-0.5528	0.1463	0.7607	0.0445	0.2299	-0.0779	0.1442	0.0774	0.014	0.0136	49.142	22.46	131.07
8	3.9468	-0.7923	-1.5546	6.1225	-1.6507	6.6444	0.3285	0.1372	0.3287	0.3881	-0.1482	0.6781	-0.2161	-0.8247	-0.1803	0.0803	-0.1091	0.1438	0.1476	-0.0497	-0.0235	36.181	18.238	132.55
9	1.4436	0.6122	-0.6452	4.4884	-0.2822	3.6147	0.265	-0.2102	0.181	0.8611	-0.384	-0.0269	-0.0366	0.208	0.119	0.3765	-0.235	0.0842	0.0638	-0.0324	-0.1139	44.429	10.099	140.357
10	5.7515	1.6101	-1.6898	3.3292	-1.0674	2.0239	0.0567	-0.0443	-0.639	0.1596	-0.499	-0.4846	0.7646	0.0247	0.4423	0.4229	-0.1093	0.0686	-0.0281	0.0547	-0.0461	49.112	-6.395	134.172
11	2.5298	0.4668	1.4563	6.4273	0.2384	7.3542	0.1057	-0.157	-0.1527	0.4745	-0.0406	0.0664	0.8776	-0.1193	-0.0651	0.3267	-0.3966	0.2488	0.1173	-0.0538	-0.0466	33.448	-3.874	140.472
12	1.3602	2.1257	-0.5313	6.385	-1.8817	3.4451	0.5915	0.2225	0.3215	0.4732	-0.0556	1.1883	0.345	-1.013	-0.5359	0.0939	-0.379	0.2366	0.1837	-0.0225	-0.0036	28.611	4.605	137.753

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	8 - 26	8 - 26
2	X-RAY DIFFRACTION	2	A	A	27 - 107	27 - 107
3	X-RAY DIFFRACTION	3	A	A	108 - 150	108 - 150
4	X-RAY DIFFRACTION	4	A	A	151 - 211	151 - 211
5	X-RAY DIFFRACTION	5	A	A	212 - 243	212 - 243
6	X-RAY DIFFRACTION	6	A	A	244 - 301	244 - 301
7	X-RAY DIFFRACTION	7	B	B	9 - 31	9 - 31
8	X-RAY DIFFRACTION	8	B	B	32 - 73	32 - 73
9	X-RAY DIFFRACTION	9	B	B	74 - 150	74 - 150
10	X-RAY DIFFRACTION	10	B	B	151 - 211	151 - 211
11	X-RAY DIFFRACTION	11	B	B	212 - 243	212 - 243
12	X-RAY DIFFRACTION	12	B	B	244 - 301	244 - 301

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