PDB-1tc5: Structural Analysis of a probable eukaryotic D-amino acid tRNA de...

ID or keywords:

Entry

Database: PDB / ID: 1tc5

Title

Structural Analysis of a probable eukaryotic D-amino acid tRNA deacylase

Components

Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA

Keywords

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

Function / homology

Function and homology information

D-aminoacyl-tRNA deacylase activity / Hydrolases; Acting on ester bonds / cytoplasm
Similarity search - Function

Biological species

Leishmania major (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.93 Å

Authors

Robien, M.A. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Citation

Journal: To be Published
Title: Structural analysis of LMAJ005534AAA, a probable eukaryotic D-amino acid tRNA deacylase from Leishmania major
Authors: Robien, M.A. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium

History

Deposition	May 20, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 8, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Jan 31, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4	Feb 14, 2024	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_struct_special_symmetry / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Remark 999

SEQUENCE NO SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF DEPOSITION.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1tc5.cif.gz	161.3 KB	Display	PDBx/mmCIF format
PDB format	pdb1tc5.ent.gz	129.1 KB	Display	PDB format
PDBx/mmJSON format	1tc5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1tc5_validation.pdf.gz	432.6 KB	Display	wwPDB validaton report
Full document	1tc5_full_validation.pdf.gz	438.8 KB	Display
Data in XML	1tc5_validation.xml.gz	35.1 KB	Display
Data in CIF	1tc5_validation.cif.gz	47 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tc/1tc5 ftp://data.pdbj.org/pub/pdb/validation_reports/tc/1tc5	HTTPS FTP

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Related structure data

Similar structure data	2uw6-d 6frx-d 4hpu-d 6qj7-d 2uw7-d 3e8e-5 6h2v-2 2vo7-d 6zfa-d 1ur1-d Search similar-shape structures by Omokage search (details) 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: Lmaj005534AAA

Similar structure data

Other databases

TargetDB: Lmaj005534AAA

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA

B: Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA

C: Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA

D: Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA

87.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA

B: Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA

defined by author&software
43.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA

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

3

D: Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA

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

Unit cell

Length a, b, c (Å)	67.479, 67.465, 174.410
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	17
Space group name H-M	P222₁

Components on special symmetry positions

ID	Model	Components
1	1	D-568- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	HIS	HIS	VAL	VAL	5	A	A	8 - 13	8 - 13
2	1	1	HIS	HIS	VAL	VAL	5	B	B	8 - 13	8 - 13
3	1	1	MET	MET	VAL	VAL	5	C	C	9 - 13	9 - 13
4	1	1	MET	MET	VAL	VAL	5	D	D	9 - 13	9 - 13
5	2	1	MET	MET	ALA	ALA	2	A	A	14 - 51	14 - 51
6	2	1	MET	MET	ALA	ALA	2	B	B	14 - 51	14 - 51
7	2	1	MET	MET	ALA	ALA	2	C	C	14 - 51	14 - 51
8	2	1	MET	MET	ALA	ALA	2	D	D	14 - 51	14 - 51
9	3	1	HIS	HIS	GLY	GLY	2	A	A	60 - 108	60 - 108
10	3	1	HIS	HIS	GLY	GLY	2	B	B	60 - 108	60 - 108
11	3	1	HIS	HIS	GLY	GLY	2	C	C	60 - 108	60 - 108
12	3	1	HIS	HIS	GLY	GLY	2	D	D	60 - 108	60 - 108
13	4	1	ARG	ARG	ARG	ARG	3	A	A	109	109
14	4	1	ARG	ARG	ARG	ARG	3	B	B	109	109
15	4	1	ARG	ARG	ARG	ARG	3	C	C	109	109
16	4	1	ARG	ARG	ARG	ARG	3	D	D	109	109
17	5	1	SER	SER	ASP	ASP	2	A	A	110 - 140	110 - 140
18	5	1	SER	SER	ASP	ASP	2	B	B	110 - 140	110 - 140
19	5	1	SER	SER	ASP	ASP	2	C	C	110 - 140	110 - 140
20	5	1	SER	SER	ASP	ASP	2	D	D	110 - 140	110 - 140
21	6	1	GLU	GLU	PRO	PRO	3	A	A	141 - 150	141 - 150
22	6	1	GLU	GLU	PRO	PRO	3	B	B	141 - 150	141 - 150
23	6	1	GLU	GLU	PRO	PRO	3	C	C	141 - 150	141 - 150
24	6	1	GLU	GLU	PRO	PRO	3	D	D	141 - 150	141 - 150
25	7	1	GLY	GLY	ILE	ILE	2	A	A	161 - 194	161 - 194
26	7	1	GLY	GLY	ILE	ILE	2	B	B	161 - 194	161 - 194
27	7	1	GLY	GLY	ILE	ILE	2	C	C	161 - 194	161 - 194
28	7	1	GLY	GLY	ILE	ILE	2	D	D	161 - 194	161 - 194
1	1	2	ARG	ARG	GLU	GLU	3	A	A	151 - 160	151 - 160
2	1	2	ARG	ARG	GLU	GLU	3	B	B	151 - 160	151 - 160
3	1	2	ARG	ARG	GLU	GLU	3	C	C	151 - 160	151 - 160
4	1	2	ARG	ARG	GLU	GLU	3	D	D	151 - 160	151 - 160

NCS ensembles :

ID
1
2

Details

First dimer: subunits A and B Second dimer: subunit C and a second part of the biological assembly generated by the two fold axis: -X+2, Y, -Z+1/2. Third dimer: subunit D and a second part of the biological assembly generated by the two fold axis: X, -Y+2, -Z.

#1: Protein	Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA Mass: 21774.877 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: L4171.5 / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR/DE3 / References: UniProt: P84066
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA

Mass: 21774.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Leishmania major (eukaryote) / Gene: L4171.5 / Plasmid: PET14B / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21STAR/DE3 / References: UniProt: P84066

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.28 Å³/Da / Density % sol: 45.69 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 200, MES, PEG3000, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9184 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2003
Radiation	Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.93→47.673 Å / Num. all: 48352 / Num. obs: 48177 / % possible obs: 79.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / B_iso Wilson estimate: 21.114 Å² / R_merge(I) obs: 0.058 / R_sym value: 0.058 / Net I/σ(I): 10.2
Reflection shell	Resolution: 1.93→2.02 Å / Redundancy: 2 % / R_merge(I) obs: 0.238 / Mean I/σ(I) obs: 2 / Num. unique all: 2478 / R_sym value: 0.238 / % possible all: 28.6

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: SeMAD model, which crystallized in a different space group (p21)

Resolution: 1.93→46.13 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.921 / SU B: 4.956 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: ISOTROPIC with TLS, monomer=TLS group
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SeMAD used to solve lower resolution crystal in a different space group. This model permitted phasing of this crystal.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2343	2487	5.2 %	RANDOM
R_work	0.19867	-	-	-
all	0.20053	45547	-	-
obs	0.20053	45547	79.09 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 21.081 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.04 Å²	0 Å²	0 Å²
2-	-	0 Å²	0 Å²
3-	-	-	-0.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.93→46.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5790	0	0	382	6172

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	5948
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	5436
X-RAY DIFFRACTION	r_angle_refined_deg	1.279	1.942	8023
X-RAY DIFFRACTION	r_angle_other_deg	0.802	3	12595
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.759	5	750
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	863
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6738
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	1270
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	1035
X-RAY DIFFRACTION	r_nbd_other	0.251	0.2	6093
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.081	0.2	3586
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	306
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.186	0.2	24
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.308	0.2	134
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.127	0.2	16
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it	1.749	4	3711
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.909	6	5952
X-RAY DIFFRACTION	r_scbond_it	3.809	6	2237
X-RAY DIFFRACTION	r_scangle_it	6.166	10	2071
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	955	tight positional	0.04	0.05
1	2	B	955	tight positional	0.04	0.05
1	3	C	955	tight positional	0.04	0.05
1	4	D	955	tight positional	0.04	0.05
2	1	A	58	tight positional	0.05	0.05
2	2	B	58	tight positional	0.05	0.05
2	3	C	58	tight positional	0.05	0.05
2	4	D	58	tight positional	0.05	0.05
1	1	A	1429	medium positional	0.26	0.5
1	2	B	1429	medium positional	0.25	0.5
1	3	C	1429	medium positional	0.24	0.5
1	4	D	1429	medium positional	0.26	0.5
1	1	A	149	loose positional	0.95	5
1	2	B	149	loose positional	1.09	5
1	3	C	149	loose positional	0.99	5
1	4	D	149	loose positional	0.98	5
2	1	A	78	loose positional	0.75	5
2	2	B	78	loose positional	0.76	5
2	3	C	78	loose positional	0.68	5
2	4	D	78	loose positional	0.76	5
1	1	A	955	tight thermal	0.14	0.5
1	2	B	955	tight thermal	0.13	0.5
1	3	C	955	tight thermal	0.14	0.5
1	4	D	955	tight thermal	0.13	0.5
2	1	A	58	tight thermal	0.09	0.5
2	2	B	58	tight thermal	0.09	0.5
2	3	C	58	tight thermal	0.09	0.5
2	4	D	58	tight thermal	0.09	0.5
1	1	A	1429	medium thermal	0.65	2
1	2	B	1429	medium thermal	0.64	2
1	3	C	1429	medium thermal	0.64	2
1	4	D	1429	medium thermal	0.68	2
1	1	A	149	loose thermal	2.17	10
1	2	B	149	loose thermal	2.48	10
1	3	C	149	loose thermal	2.26	10
1	4	D	149	loose thermal	2.24	10
2	1	A	78	loose thermal	3.15	10
2	2	B	78	loose thermal	3.36	10
2	3	C	78	loose thermal	3.72	10
2	4	D	78	loose thermal	3.41	10

LS refinement shell

Resolution: 1.93→2.034 Å / Total num. of bins used: 10 /

	R_factor	Num. reflection
R_free	0.324	129
R_work	0.301	2325

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	0.6253	0.1869	-0.0162	0.452	-0.1119	1.7218	0.0059	-0.0458	0.0479	0.0008	0.001	-0.0205	-0.2877	0.1021	-0.0069	0.0873	-0.0313	0.0104	0.0116	-0.0059	0.0517	39.939	43.4524	21.1877
2	0.4561	0.1768	-0.2288	0.7066	0.0897	1.9403	-0.0145	0.0339	-0.0209	-0.0439	0.0118	0.0602	0.0912	-0.2861	0.0028	0.0135	-0.0248	-0.0043	0.0754	0.0124	0.0503	24.0303	27.5071	22.429
3	0.84	0.1417	-0.1254	1.1005	0.2532	1.505	0.0244	-0.0108	-0.0142	-0.0089	-0.1033	0.1151	0.027	-0.2089	0.0789	0.0058	0.01	-0.0002	0.0634	-0.0265	0.0748	56.2656	1.0422	43.4967
4	1.1672	-0.0526	-0.2352	0.8399	-0.0577	1.6864	-0.087	0.0284	-0.112	0.0122	0.0164	-0.0021	0.2262	0.026	0.0706	0.0607	-0.0046	0.0208	0.0006	0.0025	0.0747	66.39	56.2427	-0.101

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 - 194	8 - 194
2	X-RAY DIFFRACTION	2	B	B	8 - 194	8 - 194
3	X-RAY DIFFRACTION	3	C	C	9 - 194	9 - 194
4	X-RAY DIFFRACTION	4	D	D	9 - 194	9 - 194

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