PDB-1yqf: Hypothetical protein from leishmania major unknown function seque...

ID or keywords:

Entry

Database: PDB / ID: 1yqf

Title

Hypothetical protein from leishmania major unknown function sequence homologue to human p32 protein

Components

hypothetical protein Lmaj011689

Keywords

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

Function / homology

Mitochondrial Matrix Protein; Chain A / Mitochondrial glycoprotein / Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / mitochondrial matrix / Roll / Alpha Beta / Putative p22 protein

Function and homology information

Biological species

Leishmania major (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.3 Å

Authors

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

Citation

Journal: To be published
Title: Hypothetical protein from leishmania major unknown function sequence homologue to human p32 protein
Authors: Caruthers, J. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

History

Deposition	Feb 1, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 22, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.3	Oct 11, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4	Feb 14, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Remark 999

SEQUENCE A SUITABLE SEQUENCE DATABASE REFERENCE WAS NOT AVAILABLE AT THE TIME OF PROCESSING.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1yqf.cif.gz	221.8 KB	Display	PDBx/mmCIF format
PDB format	pdb1yqf.ent.gz	179.5 KB	Display	PDB format
PDBx/mmJSON format	1yqf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1yqf_validation.pdf.gz	460.5 KB	Display	wwPDB validaton report
Full document	1yqf_full_validation.pdf.gz	469.7 KB	Display
Data in XML	1yqf_validation.xml.gz	39.1 KB	Display
Data in CIF	1yqf_validation.cif.gz	53.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yq/1yqf ftp://data.pdbj.org/pub/pdb/validation_reports/yq/1yqf	HTTPS FTP

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Related structure data

Similar structure data	3qv0-1 1p32-d 3jv1-1 2ppy-2 4g2s-d 5laa-d 1r8h-d 6j0l-3 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 - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: Lmaj011689AAA

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: hypothetical protein Lmaj011689

B: hypothetical protein Lmaj011689

C: hypothetical protein Lmaj011689

D: hypothetical protein Lmaj011689

E: hypothetical protein Lmaj011689

F: hypothetical protein Lmaj011689

138 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: hypothetical protein Lmaj011689

B: hypothetical protein Lmaj011689

C: hypothetical protein Lmaj011689

defined by author&software
69.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: hypothetical protein Lmaj011689

E: hypothetical protein Lmaj011689

F: hypothetical protein Lmaj011689

defined by author&software
69.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.738, 113.910, 87.858
Angle α, β, γ (deg.)	90.000, 90.489, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	hypothetical protein Lmaj011689 Mass: 23042.553 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Plasmid details: SGPP target construct Lmaj011689AAA / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Q7K6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.55 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.4 ul protein 19 mg/ml 0.4 ul crystallization buffer 20% PEG 4000, 100 mM CaCl2, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2004
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→19.035 Å / Num. all: 56510 / Num. obs: 56021 / Limit h max: 28 / Limit h min: -28 / Limit k max: 49 / Limit k min: 0 / Limit l max: 38 / Limit l min: 0

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 0.629 / Cor.coef. F_o:F_c: 0.203

	Highest resolution	Lowest resolution
Translation	4 Å	15 Å

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Processing

Software

Name	Version	Classification
EPMR	2.5	phasing
PDB_EXTRACT	1.501	data extraction
DM		phasing
REFMAC	refmac_5.1.24 24/04/2001	refinement
Blu-Ice		data collection
ELVES		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→19.035 Å / WR_factor R_free: 0.296 / WR_factor R_work: 0.278 / TLS residual ADP flag: LIKELY RESIDUAL / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection
R_free	0.2735	2824	5.04 %
R_work	0.2549	-	-
obs	-	53207	-

Displacement parameters

B_iso mean: 37.702 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.73 Å²	0 Å²	0.191 Å²
2-	-	1.035 Å²	0 Å²
3-	-	-	-1.762 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→19.035 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8643	0	0	196	8839

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.021	8809
X-RAY DIFFRACTION	r_bond_other_d	0.011	0.02	7609
X-RAY DIFFRACTION	r_angle_refined_deg	0.895	1.95	11934
X-RAY DIFFRACTION	r_angle_other_deg	0.914	3	17789
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.097	5	1075
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	1293
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	9967
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1747
X-RAY DIFFRACTION	r_nbd_refined	0.143	0.2	1586
X-RAY DIFFRACTION	r_nbd_other	0.191	0.2	8332
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	4266
X-RAY DIFFRACTION	r_nbtor_other	0.077	0.2	5155
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.094	0.2	181
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.921	0.2	50
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.459	0.2	87
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.575	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	0.611	1.5	5389
X-RAY DIFFRACTION	r_mcbond_other	0.045	1.5	2182
X-RAY DIFFRACTION	r_mcangle_it	1.134	2	8643
X-RAY DIFFRACTION	r_mcangle_other	0.599	2	7436
X-RAY DIFFRACTION	r_scbond_it	0.711	3	3420
X-RAY DIFFRACTION	r_scbond_other	0.195	3	5427
X-RAY DIFFRACTION	r_scangle_it	1.321	4.5	3291
X-RAY DIFFRACTION	r_scangle_it_other	0.639	4.5	10353

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	Num. reflection all
2.3-2.3598	0.386	212	0.329	3834	X-RAY DIFFRACTION	4163
2.36-2.4244	0.348	191	0.312	3810	X-RAY DIFFRACTION	4073
2.424-2.4946	0.34	199	0.31	3707	X-RAY DIFFRACTION	3956
2.495-2.5714	0.318	189	0.3	3585	X-RAY DIFFRACTION	3823
2.571-2.6557	0.311	179	0.313	3522	X-RAY DIFFRACTION	3744
2.656-2.7488	0.344	194	0.302	3352	X-RAY DIFFRACTION	3584
2.749-2.8525	0.328	178	0.283	3293	X-RAY DIFFRACTION	3492
2.853-2.9689	0.315	182	0.286	3134	X-RAY DIFFRACTION	3337
2.969-3.1008	0.299	172	0.278	3035	X-RAY DIFFRACTION	3218
3.101-3.2521	0.312	146	0.277	2928	X-RAY DIFFRACTION	3083
3.252-3.4278	0.284	152	0.26	2763	X-RAY DIFFRACTION	2923
3.428-3.6355	0.281	120	0.253	2633	X-RAY DIFFRACTION	2756
3.636-3.8862	0.248	136	0.234	2467	X-RAY DIFFRACTION	2606
3.886-4.1972	0.27	116	0.228	2295	X-RAY DIFFRACTION	2416
4.197-4.5972	0.211	98	0.212	2143	X-RAY DIFFRACTION	2245
4.597-5.1387	0.209	96	0.209	1917	X-RAY DIFFRACTION	2020
5.139-5.9316	0.253	83	0.265	1707	X-RAY DIFFRACTION	1793
5.932-7.2596	0.264	68	0.256	1462	X-RAY DIFFRACTION	1535
7.26-10.245	0.21	81	0.196	1092	X-RAY DIFFRACTION	1176
10.245-111.8034	0.186	32	0.195	530	X-RAY DIFFRACTION	680

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	0.1661	-0.0275	-0.1357	2.0355	0.6935	0.2986	-0.0864	0.047	0.0255	-0.1245	0.1486	-0.0685	-0.0763	0.0179	-0.0622	0.084	-0.0076	-0.0117	0.1385	0.0098	0.1047	2.6962	1.9928	0.8946
2	0.5652	-0.0621	0.0596	2.6739	-1.6185	0.7828	-0.0246	-0.068	0.0908	0.4811	0.0349	-0.0406	-0.1957	-0.0633	-0.0103	0.1727	0.0515	0.0143	0.0944	-0.0558	0.0497	2.2221	2.4385	32.8119
3	0.0194	0.0911	-0.2263	0.4988	-0.0609	2.1635	-0.0091	0.0101	0.0609	0.0107	-0.0056	-0.0203	-0.1461	0.0118	0.0148	0.0364	-0.0152	0.0021	0.1187	0.0038	0.1354	31.3002	-17.1815	-27.2204
4	0.0753	-0.0764	0.1188	2.1081	-0.7197	0.2739	-0.0781	0.0403	-0.0201	-0.1405	0.1561	0.0634	0.0909	-0.0083	-0.0779	0.0996	-0.0061	0.0055	0.1315	-0.0046	0.1107	30.0473	-44.9585	-43.0478
5	0.4954	0.1495	-0.0939	2.7183	1.4689	1.0068	-0.0414	-0.0666	-0.0764	0.4508	0.0273	0.0706	0.2139	0.104	0.0141	0.1599	0.049	-0.0245	0.0737	0.0376	0.0585	29.82	-45.3285	-11.0956
6	0.1792	0.052	0.2119	0.5829	0.0156	2.1046	-0.0084	-0.0017	-0.0684	0.0165	-0.0012	0.0193	0.1257	-0.0447	0.0095	0.0347	-0.0148	-0.0086	0.1109	-0.0019	0.1265	1.1546	-25.8014	16.8553
7	0.0278	-0.0172	0.007	0.087	0.0778	0.2335	-0.0209	-0.0028	0.0004	-0.0104	0.0148	0.0126	0.0117	0.0065	0.0062	0.07	0.0102	-0.012	0.1199	0.0043	0.1414	15.1762	-20.3334	-8.7919

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	14 - 195
2	X-RAY DIFFRACTION	2	B	14 - 195
3	X-RAY DIFFRACTION	3	F	15 - 195
4	X-RAY DIFFRACTION	4	D	14 - 195
5	X-RAY DIFFRACTION	5	E	14 - 195
6	X-RAY DIFFRACTION	6	C	14 - 195
7	X-RAY DIFFRACTION	7	A	196 - 244
8	X-RAY DIFFRACTION	7	B	196 - 209
9	X-RAY DIFFRACTION	7	C	196 - 238
10	X-RAY DIFFRACTION	7	D	196 - 237
11	X-RAY DIFFRACTION	7	E	196 - 202
12	X-RAY DIFFRACTION	7	F	196 - 236

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