PDB-3m4s: Crystal structure of a putative endoribonuclease L-PSP from Entam...

ID or keywords:

Entry

Database: PDB / ID: 3m4s

Title

Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica, orthorhombic form

Components

putative Endoribonuclease L-PSP

Keywords

UNKNOWN FUNCTION / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

deaminase activity / mitochondrion / cytosol
Similarity search - Function

Biological species

Entamoeba histolytica (eukaryote)

Method

X-RAY DIFFRACTION /

molecular replacement,

molecular replacement / Resolution: 2.3 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica, orthorhombic form
Authors: Gardberg, A. / Abendroth, J. / Davies, D. / Staker, B.

History

Deposition	Mar 11, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 31, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Feb 21, 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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	3m4s.cif.gz	147.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3m4s_validation.pdf.gz	475.3 KB	Display	wwPDB validaton report
Full document	3m4s_full_validation.pdf.gz	480.8 KB	Display
Data in XML	3m4s_validation.xml.gz	27.7 KB	Display
Data in CIF	3m4s_validation.cif.gz	38.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m4/3m4s ftp://data.pdbj.org/pub/pdb/validation_reports/m4/3m4s	HTTPS FTP

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Related structure data

Related structure data	3m1x
Similar structure data	2uyp-d 3l7q-3 6zrz-2 5yu2-1 4okz-4 2uyk-d 5v4d-2 2csl-2 5k9m-d 3ko5-1 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: EnhiA.00579.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (1)

Deposited unit

A: putative Endoribonuclease L-PSP

B: putative Endoribonuclease L-PSP

C: putative Endoribonuclease L-PSP

D: putative Endoribonuclease L-PSP

E: putative Endoribonuclease L-PSP

F: putative Endoribonuclease L-PSP

hetero molecules

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

1

A: putative Endoribonuclease L-PSP

B: putative Endoribonuclease L-PSP

C: putative Endoribonuclease L-PSP

hetero molecules

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

2

D: putative Endoribonuclease L-PSP

E: putative Endoribonuclease L-PSP

F: putative Endoribonuclease L-PSP

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

Unit cell

Length a, b, c (Å)	102.600, 110.490, 52.920
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-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	ALA	ALA	GLY	GLY	1	A	A	22 - 36	43 - 57
2	1	ALA	ALA	GLY	GLY	1	B	B	22 - 36	43 - 57
3	1	ALA	ALA	GLY	GLY	1	C	C	22 - 36	43 - 57
4	1	ALA	ALA	GLY	GLY	1	D	D	22 - 36	43 - 57
5	1	ALA	ALA	GLY	GLY	1	E	E	22 - 36	43 - 57
6	1	ALA	ALA	GLY	GLY	1	F	F	22 - 36	43 - 57
1	2	LEU	LEU	LYS	LYS	1	A	A	64 - 73	85 - 94
2	2	LEU	LEU	LYS	LYS	1	B	B	64 - 73	85 - 94
3	2	LEU	LEU	LYS	LYS	1	C	C	64 - 73	85 - 94
4	2	LEU	LEU	LYS	LYS	1	D	D	64 - 73	85 - 94
5	2	LEU	LEU	LYS	LYS	1	E	E	64 - 73	85 - 94
6	2	LEU	LEU	LYS	LYS	1	F	F	64 - 73	85 - 94
1	3	VAL	VAL	GLN	GLN	4	A	A	6 - 21	27 - 42
2	3	VAL	VAL	GLN	GLN	4	B	B	6 - 21	27 - 42
3	3	VAL	VAL	GLN	GLN	4	C	C	6 - 21	27 - 42
4	3	VAL	VAL	GLN	GLN	4	D	D	6 - 21	27 - 42
5	3	VAL	VAL	GLN	GLN	4	E	E	6 - 21	27 - 42
6	3	VAL	VAL	GLN	GLN	4	F	F	6 - 21	27 - 42
1	4	GLY	GLY	VAL	VAL	4	A	A	46 - 63	67 - 84
2	4	GLY	GLY	VAL	VAL	4	B	B	46 - 63	67 - 84
3	4	GLY	GLY	VAL	VAL	4	C	C	46 - 63	67 - 84
4	4	GLY	GLY	VAL	VAL	4	D	D	46 - 63	67 - 84
5	4	GLY	GLY	VAL	VAL	4	E	E	46 - 63	67 - 84
6	4	GLY	GLY	VAL	VAL	4	F	F	46 - 63	67 - 84
1	5	VAL	VAL	ASP	ASP	4	A	A	74 - 83	95 - 104
2	5	VAL	VAL	ASP	ASP	4	B	B	74 - 83	95 - 104
3	5	VAL	VAL	ASP	ASP	4	C	C	74 - 83	95 - 104
4	5	VAL	VAL	ASP	ASP	4	D	D	74 - 83	95 - 104
5	5	VAL	VAL	ASP	ASP	4	E	E	74 - 83	95 - 104
6	5	VAL	VAL	ASP	ASP	4	F	F	74 - 83	95 - 104
1	6	ALA	ALA	LEU	LEU	4	A	A	97 - 127	118 - 148
2	6	ALA	ALA	LEU	LEU	4	B	B	97 - 127	118 - 148
3	6	ALA	ALA	LEU	LEU	4	C	C	97 - 127	118 - 148
4	6	ALA	ALA	LEU	LEU	4	D	D	97 - 127	118 - 148
5	6	ALA	ALA	LEU	LEU	4	E	E	97 - 127	118 - 148
6	6	ALA	ALA	LEU	LEU	4	F	F	97 - 127	118 - 148

#1: Protein	putative Endoribonuclease L-PSP Mass: 15640.977 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EHI_087570 / Plasmid: AVA0421 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4LXT9
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 121 / 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 grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: INDEX SCREEN CONDITION F10: 0.2 M NaCl, 25% PEG 3350, ENHIA.00579.A AT 25.8 MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
Detector	Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 19, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.3→29.08 Å / Num. all: 27516 / Num. obs: 26517 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / B_iso Wilson estimate: 34.83 Å² / R_merge(I) obs: 0.085 / Net I/σ(I): 14.58
Reflection shell	Resolution: 2.3→2.36 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.498 / Mean I/σ(I) obs: 2.6 / % possible all: 95

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

molecular replacement,

molecular replacement
Resolution: 2.3→29 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.902 / SU B: 24.052 / SU ML: 0.25 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.711 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.273	1353	5.1 %	RANDOM
R_work	0.213	-	-	-
obs	0.216	26478	-	-
all	-	27516	-	-

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: 10.6 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.29 Å²	0 Å²	0 Å²
2-	-	-1.13 Å²	0 Å²
3-	-	-	1.42 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5435	0	1	121	5557

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	5543
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3569
X-RAY DIFFRACTION	r_angle_refined_deg	1.443	1.977	7522
X-RAY DIFFRACTION	r_angle_other_deg	0.808	3	8834
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.318	5	759
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.706	25.729	192
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.862	15	901
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.472	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	895
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6296
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1031
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.504	1.5	3737
X-RAY DIFFRACTION	r_mcbond_other	0.133	1.5	1546
X-RAY DIFFRACTION	r_mcangle_it	0.934	2	5932
X-RAY DIFFRACTION	r_scbond_it	1.555	3	1806
X-RAY DIFFRACTION	r_scangle_it	2.565	4.5	1584
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
A	285	tight positional	0.46	0.05
B	285	tight positional	0.24	0.05
C	285	tight positional	0.18	0.05
D	285	tight positional	0.21	0.05
E	285	tight positional	0.18	0.05
F	285	tight positional	0.21	0.05
A	864	medium positional	0.26	0.5
B	864	medium positional	0.32	0.5
C	864	medium positional	0.22	0.5
D	864	medium positional	0.25	0.5
E	864	medium positional	0.31	0.5
F	864	medium positional	0.25	0.5
A	285	tight thermal	0.48	0.5
B	285	tight thermal	0.5	0.5
C	285	tight thermal	0.51	0.5
D	285	tight thermal	0.61	0.5
E	285	tight thermal	0.52	0.5
F	285	tight thermal	0.51	0.5
A	864	medium thermal	0.52	2
B	864	medium thermal	0.54	2
C	864	medium thermal	0.49	2
D	864	medium thermal	0.53	2
E	864	medium thermal	0.58	2
F	864	medium thermal	0.59	2

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.365	92	-
R_work	0.278	1786	-
obs	-	-	94.94 %

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	2.445	-0.1003	0.054	1.1371	0.6442	1.5503	-0.0115	0.0536	-0.0857	-0.2027	0.0126	0.1053	-0.2171	0.0023	-0.0011	0.1596	-0.0293	-0.0773	0.0051	0.0291	0.0889	-9.304	28.815	-35.292
2	2.1983	-0.138	-0.0161	0.6748	-0.1094	1.0174	-0.0246	-0.0842	0.0617	0.0762	-0.0325	-0.0012	-0.0832	0.0864	0.0572	0.1362	-0.0688	-0.0449	0.0571	-0.0019	0.0693	9.159	34.995	-22.944
3	2.1829	0.2015	-0.1191	2.6177	-0.6252	1.1664	0.1217	-0.2279	-0.4092	0.0419	0.0153	-0.0085	0.0016	-0.0536	-0.137	0.0895	-0.0613	-0.094	0.0633	0.0808	0.1738	-2.705	15.857	-17.792
4	1.8257	-0.2969	0.0674	3.9997	-0.2455	1.0279	-0.0168	-0.2777	0.2135	0.4377	0.3961	-0.8988	0.3189	0.1206	-0.3793	0.1322	0.0907	-0.2106	0.1152	-0.1985	0.3768	-16.373	-1.15	7.431
5	1.6055	-0.2071	-0.1622	3.865	0.6079	1.5148	0.0366	0.0626	0.0401	-0.5457	0.1753	-0.172	0.0737	-0.0763	-0.2119	0.1468	-0.038	-0.009	0.0477	-0.0361	0.06	-29.152	-7.384	-10.625
6	1.6161	-0.6607	-0.1307	3.3268	0.7896	1.7512	-0.0748	-0.2278	0.1716	-0.0621	0.1028	0.0364	-0.1485	-0.0832	-0.028	0.0179	0.0311	-0.0206	0.0746	-0.0689	0.1154	-34.245	11.716	0.923

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 127
2	X-RAY DIFFRACTION	2	B	3 - 127
3	X-RAY DIFFRACTION	3	C	3 - 127
4	X-RAY DIFFRACTION	4	D	3 - 127
5	X-RAY DIFFRACTION	5	E	3 - 127
6	X-RAY DIFFRACTION	6	F	2 - 127

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