PDB-6vmt: Leishmania major Programmed Cell Death Protein 5 Homolog

ID or keywords:

Entry

Database: PDB / ID: 6vmt

Title

Leishmania major Programmed Cell Death Protein 5 Homolog

Components

Programmed Cell Death Protein 5 Homolog

Keywords

DNA BINDING PROTEIN /

Structural Genomics / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / PSI-2 /

Protein Structure Initiative

Function / homology

PDCD5-like / PDCD5-like superfamily / Double-stranded DNA-binding domain /

DNA binding /

nucleus /

cytosol / Uncharacterized protein

Function and homology information

Biological species

Leishmania major (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.501 Å

Authors

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

Citation

Journal: To be published
Title: Leishmania major Programmed Cell Death Protein 5 Homolog
Authors: Merritt, E.A. / Anderson, L. / Arakaki, T. / Hol, W.G. / Le Trong, I. / Mehlin, C. / Soltis, M. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

History

Deposition	Jan 28, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 26, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6vmt.cif.gz	35.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6vmt.ent.gz	21.3 KB	Display	PDB format
PDBx/mmJSON format	6vmt.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/vm/6vmt ftp://data.pdbj.org/pub/pdb/validation_reports/vm/6vmt	HTTPS FTP

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Related structure data

Related structure data	6iqoS S: Starting model for refinement
Similar structure data	5ms5-2 1he7-d 3qb4-2 6sf1-d 1wwa-2 6iqo-2 2ekh-d 4b8t-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
Other databases	TargetTrack: SGPP-Lmaj003759

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Programmed Cell Death Protein 5 Homolog

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	115.386, 115.386, 58.628
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	155
Space group name H-M	H32

#1: Protein	Programmed Cell Death Protein 5 Homolog / Mass: 13304.014 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_28_1920 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Q874
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.82 Å³/Da / Density % sol: 56.43 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 1.5 M K2HPO4

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.2 / Wavelength: 0.95373,0.97962,0.97949

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2005

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.95373	1
2	0.97962	1
3	0.97949	1

Reflection

Resolution: 2.5→25.296 Å / Num. obs: 4643 / % possible obs: 87.8 % / Redundancy: 8.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.114 / R_pim(I) all: 0.04 / R_rim(I) all: 0.122 / Net I/σ(I): 11.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
2.5-2.6	6.9	6.236	306	0.264	2.424	6.752	53.5
9.01-25.296	8.9	0.074	122	0.999	0.025	0.078	95.2

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Processing

Software

Name	Version	Classification
Aimless	0.7.4	data scaling
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.25	data extraction
MOSFLM		data reduction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6IQO

6iqo

Resolution: 2.501→25.296 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.919 / SU B: 11.938 / SU ML: 0.242 / Cross valid method: FREE R-VALUE / ESU R: 0.471 / ESU R Free: 0.306
Details: Hydrogens have been added in their riding positions. Sulfur f'' term set to 2.5e to account for partial substitution of SeMet for Met

	R_factor	Num. reflection	% reflection
R_free	0.2727	194	4.181 %
R_work	0.2223	-	-
all	0.224	-	-
obs	-	4640	87.829 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å

Displacement parameters

B_iso mean: 79.593 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.435 Å²	-0.218 Å²	0 Å²
2-	-	-0.435 Å²	0 Å²
3-	-	-	1.412 Å²

Refinement step

Cycle: LAST / Resolution: 2.501→25.296 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	783	0	0	16	799

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	788
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	748
X-RAY DIFFRACTION	r_angle_refined_deg	1.605	1.647	1052
X-RAY DIFFRACTION	r_angle_other_deg	1.262	1.577	1743
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.778	5	98
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.103	22.642	53
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.702	15	163
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.708	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	101
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	890
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	149
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	176
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	673
X-RAY DIFFRACTION	r_nbtor_refined	0.153	0.2	372
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	425
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	20
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.258	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.227	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.142	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	7.567	7.783	395
X-RAY DIFFRACTION	r_mcbond_other	7.344	7.773	394
X-RAY DIFFRACTION	r_mcangle_it	9.843	11.721	492
X-RAY DIFFRACTION	r_mcangle_other	9.834	11.74	493
X-RAY DIFFRACTION	r_scbond_it	9.396	9.382	393
X-RAY DIFFRACTION	r_scbond_other	9.385	9.389	394
X-RAY DIFFRACTION	r_scangle_it	14.901	13.554	560
X-RAY DIFFRACTION	r_scangle_other	14.887	13.563	561
X-RAY DIFFRACTION	r_lrange_it	17.389	94.379	856
X-RAY DIFFRACTION	r_lrange_other	17.382	94.474	857

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 (%)
2.501-2.566	0.364	9	0.355	201	X-RAY DIFFRACTION	53.435
2.566-2.636	0.546	10	0.359	192	X-RAY DIFFRACTION	55.647
2.636-2.713	0.273	8	0.356	224	X-RAY DIFFRACTION	64.444
2.713-2.796	0.436	9	0.352	242	X-RAY DIFFRACTION	69.916
2.796-2.887	0.562	11	0.308	286	X-RAY DIFFRACTION	86.842
2.887-2.988	0.321	18	0.279	315	X-RAY DIFFRACTION	99.701
2.988-3.101	0.452	16	0.29	309	X-RAY DIFFRACTION	100
3.101-3.227	0.244	9	0.273	307	X-RAY DIFFRACTION	99.685
3.227-3.37	0.24	16	0.245	274	X-RAY DIFFRACTION	100
3.37-3.534	0.247	15	0.212	269	X-RAY DIFFRACTION	100
3.534-3.724	0.218	6	0.196	265	X-RAY DIFFRACTION	100
3.724-3.949	0.244	10	0.207	250	X-RAY DIFFRACTION	100
3.949-4.221	0.19	11	0.175	232	X-RAY DIFFRACTION	99.59
4.221-4.557	0.193	6	0.19	223	X-RAY DIFFRACTION	100
4.557-4.989	0.248	5	0.206	207	X-RAY DIFFRACTION	100
4.989-5.572	0.45	13	0.249	173	X-RAY DIFFRACTION	99.465
5.572-6.424	0.411	8	0.239	170	X-RAY DIFFRACTION	99.441
6.424-7.844	0.203	8	0.194	132	X-RAY DIFFRACTION	97.902
7.844-10.992	0.195	5	0.176	111	X-RAY DIFFRACTION	99.145
10.992-25.296	0.064	1	0.222	64	X-RAY DIFFRACTION	89.041

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