PDB-4tyz: Crystal structure of the C-terminal domain of an unknown protein ...

ID or keywords:

Entry

Database: PDB / ID: 4tyz

Title

Crystal structure of the C-terminal domain of an unknown protein from Leishmania infantum

Components

Uncharacterized protein

Keywords

UNKNOWN FUNCTION / SSGCID /

Leishmania infantum /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

Membrane-anchored lipid-binding protein Ysp2/Lam4-like /

domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins /

GRAM domain /

GRAM domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology

Biological species

Leishmania infantum (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.6 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of the C-terminal domain of an unknown protein from Leishmania infantum
Authors: Fischer, E. / Dranow, D.M. / Abendroth, J. / Lorimer, D. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

History

Deposition	Jul 9, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 6, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 22, 2014	Group: Database references
Revision 1.2	Feb 4, 2015	Group: Derived calculations
Revision 1.3	Nov 22, 2017	Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4	Dec 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4tyz.cif.gz	111.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4tyz.ent.gz	85.3 KB	Display	PDB format
PDBx/mmJSON format	4tyz.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/ty/4tyz ftp://data.pdbj.org/pub/pdb/validation_reports/ty/4tyz	HTTPS FTP

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Related structure data

Similar structure data	7a6x-d 6rcj-d 2ogb-2 3bkr-d 7kjo-2 6nft-2 6h8m-2 6r0q-1 7k3k-d 1oay-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-LeinA.18749.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

25.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein

hetero molecules

defined by author&software
12.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Uncharacterized protein

defined by author&software
12.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	58.860, 58.860, 135.120
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-1177- HOH
2	1	B-866- HOH

#1: Protein	Uncharacterized protein Mass: 12667.420 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 621-730) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: LINJ_30_2720 / Plasmid: LeinA.18749.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4I5U9
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.68	54
2	2.68	54

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
290	1	vapor diffusion, sitting drop	9	Reagents JCSG+ sceen b3: 20% PEG 6000, 100mM Bicine pH 9.0; LeinA.18749.a.B1.PS02018 at 8.28mg/ml
290	2	vapor diffusion, sitting drop	7.5	RigakuReagents JCSG+ sceen a9: 20% PEG 3350, 200mM Ammonium chloride; LeinA.18749.a.B1.PS02018 at 8.28mg/ml; the crystal was soaked for 10sec each in reservoir solution with 10% EG/500mM NaI, 20% EG/1000mM NaI, this sample was used for in-house phasing

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Data collection

Diffraction

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

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-F		1	0.97872
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 13, 2014

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Diamond [111]	SINGLE WAVELENGTH	M	x-ray	1
2	GRAPHITE	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97872	1
2	1.5418	1

Reflection

Number: 185526 / R_merge(I) obs: 0.068 / Χ²: 1.2 / D res high: 2 Å / Num. obs: 34864 / % possible obs: 99.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	ID	R_merge(I) obs
8.94	50	399	1	0.019
6.32	8.94	712	1	0.037
5.16	6.32	937	1	0.037
4.47	5.16	1099	1	0.027
4	4.47	1259	1	0.027
3.65	4	1366	1	0.029
3.38	3.65	1523	1	0.036
3.16	3.38	1624	1	0.045
2.98	3.16	1689	1	0.061
2.83	2.98	1850	1	0.079
2.7	2.83	1908	1	0.092
2.58	2.7	1998	1	0.11
2.48	2.58	2067	1	0.141
2.39	2.48	2191	1	0.171
2.31	2.39	2241	1	0.163
2.24	2.31	2332	1	0.165
2.17	2.24	2389	1	0.186
2.11	2.17	2442	1	0.193
2.05	2.11	2476	1	0.209
2	2.05	2362	1	0.227

Reflection

Resolution: 1.6→50 Å / Num. all: 36702 / Num. obs: 36500 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / B_iso Wilson estimate: 13.71 Å² / R_merge F obs: 1 / R_merge(I) obs: 0.048 / R_rim(I) all: 0.052 / R_sym value: 0.048 / Χ²: 0.968 / Net I/σ(I): 30.88 / Num. measured all: 265399

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.6-1.64	7.29	0.879	0.522	3.73	19463	2670	2669	0.562	100
1.64-1.69		0.919	0.411	4.8	18998	2601	2601	0.443	100
1.69-1.74		0.951	0.323	6.02	18500	2538	2538	0.347	100
1.74-1.79		0.971	0.241	7.92	17914	2447	2446	0.259	100
1.79-1.85		0.982	0.187	10.08	17500	2398	2397	0.202	100
1.85-1.91		0.989	0.147	12.97	16796	2303	2303	0.158	100
1.91-1.98		0.995	0.11	16.94	16420	2231	2231	0.118	100
1.98-2.07		0.996	0.084	22.14	15691	2149	2149	0.09	100
2.07-2.16		0.998	0.064	28.31	15215	2077	2072	0.069	99.8
2.16-2.26		0.999	0.053	33.06	14724	2003	1998	0.057	99.8
2.26-2.39		0.999	0.047	36.66	13688	1875	1872	0.05	99.8
2.39-2.53		0.999	0.042	40.75	13062	1784	1778	0.045	99.7
2.53-2.7		0.999	0.035	48.25	12391	1703	1690	0.038	99.2
2.7-2.92		0.999	0.03	56.9	11553	1593	1579	0.032	99.1
2.92-3.2		1	0.025	66.29	10423	1462	1448	0.027	99
3.2-3.58		1	0.021	77.74	9478	1330	1313	0.023	98.7
3.58-4.13		1	0.018	85.01	8366	1201	1185	0.019	98.7
4.13-5.06		1	0.016	90.68	7055	1018	996	0.017	97.8
5.06-7.16		1	0.018	84.9	5506	818	792	0.019	96.8
7.16-50		1	0.017	83.99	2656	501	443	0.019	88.4

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
XDS		data scaling
XSCALE		data scaling
PHASER		phasing
PDB_EXTRACT	3.14	data extraction
ARP		model building
PHENIX	(phenix.refine: dev_1738)	refinement
CNS		refinement

Refinement

Method to determine structure:

SAD / Resolution: 1.6→33.752 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1862	1909	5.23 %	Random selection
R_work	0.1585	34570	-	-
obs	0.16	36479	99.57 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 58.02 Å² / B_iso mean: 19.8652 Å² / B_iso min: 6.41 Å²

Refinement step

Cycle: final / Resolution: 1.6→33.752 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1743	0	4	296	2043
B_iso mean	-	-	16.06	34.72	-
Num. residues	-	-	-	-	218

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	1886
X-RAY DIFFRACTION	f_angle_d	1.022	2580
X-RAY DIFFRACTION	f_chiral_restr	0.042	291
X-RAY DIFFRACTION	f_plane_restr	0.005	326
X-RAY DIFFRACTION	f_dihedral_angle_d	13.559	685

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.64	0.2301	127	0.2047	2450	2577	100
1.64-1.6844	0.2322	136	0.1892	2420	2556	100
1.6844-1.7339	0.2223	144	0.1768	2456	2600	100
1.7339-1.7899	0.1832	121	0.1641	2444	2565	100
1.7899-1.8539	0.178	122	0.1616	2455	2577	100
1.8539-1.9281	0.1743	134	0.1541	2446	2580	100
1.9281-2.0158	0.1685	121	0.1535	2460	2581	100
2.0158-2.1221	0.2078	146	0.1489	2468	2614	100
2.1221-2.255	0.1722	147	0.1561	2444	2591	100
2.255-2.4291	0.1826	161	0.1614	2449	2610	100
2.4291-2.6734	0.2169	147	0.1669	2480	2627	100
2.6734-3.0601	0.2025	140	0.164	2469	2609	99
3.0601-3.8545	0.1645	120	0.1434	2539	2659	99
3.8545-33.7596	0.1699	143	0.1543	2590	2733	97

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	0.5553	0.0931	-0.1667	0.6812	-0.5854	1.6265	0.0731	0.1115	-0.0242	-0.1415	-0.1002	-0.1698	0.0849	0.1029	-0.0013	0.1178	0.048	0.0508	0.103	0.0331	0.1468	-38.0208	28.1925	21.3668
2	1.307	-0.0788	0.3478	1.8147	-1.1733	1.9499	0.0481	0.0501	0.022	-0.0213	-0.0804	-0.0155	-0.1406	-0.0689	0.0157	0.111	0.0458	0.0303	0.1081	0.0194	0.09	-46.0205	35.7389	26.8474
3	0.9792	0.7846	-0.7749	1.0019	0.3493	3.0971	0.1876	0.1825	-0.1034	0.121	0.0576	-0.323	-0.0047	0.1927	-0.109	0.2048	0.1118	0.0455	0.2745	0.0719	0.2513	-42.357	46.2155	8.7329
4	1.9435	0.1331	-0.3396	1.5826	0.2916	4.9737	0.1003	0.0302	0.2655	0.0331	-0.0995	-0.1346	-0.2955	-0.081	-0.0326	0.1353	0.0537	0.0463	0.1107	0.0421	0.1261	-42.8186	40.3643	21.2454
5	2.8917	0.1989	-0.1555	4.4048	-0.8175	4.362	0.1962	0.4519	-0.1922	-0.1457	-0.0294	0.2949	-0.1934	-0.527	-0.1217	0.1066	0.0591	-0.0006	0.1349	-0.011	0.1731	-51.8006	33.6645	18.0462
6	0.9536	0.686	0.0482	1.1873	0.2318	1.6199	-0.0026	-0.0817	0.0335	0.1238	0.0056	0.1199	-0.0068	-0.1597	0.0009	0.0773	0.0079	0.0373	0.0974	-0.0112	0.0949	-20.5116	28.9399	0.0366
7	0.4118	-0.7192	-0.2944	1.4376	1.0853	1.9425	-0.1626	0.0196	-0.115	0.1726	0.0511	0.2585	0.1701	-0.2993	0.1243	0.2039	-0.0265	0.0586	0.2435	-0.0655	0.1563	-15.602	45.0387	13.8562
8	3.6375	0.0941	-1.7276	3.0338	-0.6643	6.5507	0.15	0.0405	0.2707	-0.0114	0.0164	0.2357	-0.449	-0.0995	-0.1127	0.1277	0.0019	0.031	0.1165	-0.0567	0.1076	-16.4509	39.4064	1.4319
9	3.306	0.0346	0.1305	5.1977	0.4825	3.2379	0.0995	-0.3657	-0.3366	0.1427	-0.0783	-0.4071	-0.1884	0.3625	-0.0774	0.0811	-0.0205	-0.0166	0.0993	-0.0039	0.149	-8.1943	31.3704	4.3779

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 621 through 673 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 674 through 687 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 688 through 697 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 698 through 715 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 716 through 729 )	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 621 through 687 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 688 through 697 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 698 through 715 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 716 through 729 )	B

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