PDB-3vcz: 1.80 Angstrom resolution crystal structure of a putative translat...

ID or keywords:

Entry

Database: PDB / ID: 3vcz

Title

1.80 Angstrom resolution crystal structure of a putative translation initiation inhibitor from Vibrio vulnificus CMCP6

Components

Endoribonuclease L-PSP

Keywords

TRANSLATION / Virulence / Pathogenesis / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

metal ion binding
Similarity search - Function

Biological species

Vibrio vulnificus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Halavaty, A.S. / Minasov, G. / Filippova, E.V. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: 1.80 Angstrom resolution crystal structure of a putative translation initiation inhibitor from Vibrio vulnificus CMCP6
Authors: Halavaty, A.S. / Minasov, G. / Filippova, E.V. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jan 4, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.2	Sep 13, 2023	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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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	3vcz.cif.gz	179.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3vcz.ent.gz	143.8 KB	Display	PDB format
PDBx/mmJSON format	3vcz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3vcz_validation.pdf.gz	462.8 KB	Display	wwPDB validaton report
Full document	3vcz_full_validation.pdf.gz	465.4 KB	Display
Data in XML	3vcz_validation.xml.gz	20.4 KB	Display
Data in CIF	3vcz_validation.cif.gz	29.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vc/3vcz ftp://data.pdbj.org/pub/pdb/validation_reports/vc/3vcz	HTTPS FTP

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Related structure data

Related structure data	1qu9S S: Starting model for refinement
Similar structure data	2uyn-d 3r0p-2 2uyp-d 5yu2-1 4okm-1 5jxm-d 4w89-2 6zry-2 3vxd-4 3r0p-1 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	TargetTrack: IDP91387

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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: Endoribonuclease L-PSP

B: Endoribonuclease L-PSP

C: Endoribonuclease L-PSP

hetero molecules

50.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

2

A: Endoribonuclease L-PSP

B: Endoribonuclease L-PSP

C: Endoribonuclease L-PSP

hetero molecules

A: Endoribonuclease L-PSP

B: Endoribonuclease L-PSP

C: Endoribonuclease L-PSP

hetero molecules

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

Unit cell

Length a, b, c (Å)	71.877, 86.580, 68.162
Angle α, β, γ (deg.)	90.00, 90.67, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-201- CA

#1: Protein	Endoribonuclease L-PSP / Putative translation initiation inhibitor Mass: 16446.471 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: VV1_1463 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/Magic / References: UniProt: Q8DCF8, UniProt: A0A3Q0L3N0*PLUS
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.15 Å³/Da / Density % sol: 42.77 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Protein: 7.5 mg/mL in 10 mM Tris-HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystallization: The JCSG+ Suite (condition D11: 0.14 M CaCl2, 0.07 M Na acetate pH 4.6, 14 % (v/v) isopropanol, 30 % (v/v) ...Details: Protein: 7.5 mg/mL in 10 mM Tris-HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystallization: The JCSG+ Suite (condition D11: 0.14 M CaCl2, 0.07 M Na acetate pH 4.6, 14 % (v/v) isopropanol, 30 % (v/v) glycerol) , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal

Density Matthews: 2.15 Å³/Da / Density % sol: 42.77 %

Crystal grow

Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Protein: 7.5 mg/mL in 10 mM Tris-HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystallization: The JCSG+ Suite (condition D11: 0.14 M CaCl2, 0.07 M Na acetate pH 4.6, 14 % (v/v) isopropanol, 30 % (v/v) ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.99984 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2011 / Details: mirror
Radiation	Monochromator: Si(111)Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99984 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. all: 38405 / Num. obs: 38405 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / R_merge(I) obs: 0.057 / Net I/σ(I): 20.78
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.39 / Mean I/σ(I) obs: 2.64 / % possible all: 94

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHASER		phasing
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1QU9

1qu9

Resolution: 1.8→29.13 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.961 / SU B: 4.777 / SU ML: 0.068 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18286	1923	5 %	RANDOM
R_work	0.15516	-	-	-
obs	0.1566	36476	99.33 %	-
all	-	36476	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 21.685 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.9 Å²	-0 Å²	-0.18 Å²
2-	-	-1.8 Å²	-0 Å²
3-	-	-	-1.1 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→29.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2832	0	57	314	3203

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	3160
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2039
X-RAY DIFFRACTION	r_angle_refined_deg	1.487	1.961	4324
X-RAY DIFFRACTION	r_angle_other_deg	0.846	3	5042
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	1.308	5	425
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	23.425	25.474	137
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	6.805	15	489
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	6.227	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	500
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	3653
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	582
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	0.559	1.5	2040
X-RAY DIFFRACTION	r_mcbond_other	0.143	1.5	818
X-RAY DIFFRACTION	r_mcangle_it	1.037	2	3335
X-RAY DIFFRACTION	r_scbond_it	1.853	3	1120
X-RAY DIFFRACTION	r_scangle_it	3.158	4.5	989
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.266	139	-
R_work	0.237	2448	-
obs	-	-	91.22 %

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	4.8173	1.1947	4.5306	3.5824	2.6988	6.0624	-0.2272	0.0037	0.4417	-0.3668	-0.0606	-0.0326	-0.6979	-0.2863	0.2878	0.2581	0.0206	0.0082	0.1197	0.0491	0.118	12.1696	25.2048	10.1698
2	1.287	0.3854	-0.5457	1.3626	-0.1701	2.0692	-0.0097	0.1443	0.0182	-0.2627	-0.0047	-0.0676	-0.1538	-0.0009	0.0145	0.0752	0.0229	0.0137	0.0726	0.0091	0.0085	7.118	14.0132	9.5441
3	3.2227	0.1007	-0.6794	1.5441	-0.887	6.6465	0.1854	0.1976	0.0408	-0.188	-0.1059	-0.0237	0.1442	0.0787	-0.0795	0.0977	0.0362	-0.0097	0.076	-0.0162	0.011	5.2415	2.7667	4.9077
4	1.4252	-0.3545	-1.0642	1.0882	0.3698	2.5275	0.0647	0.0296	0.0831	-0.1348	-0.0347	-0.0746	-0.1648	0.1087	-0.0301	0.0263	0.0096	0.002	0.0779	-0.0047	0.0491	6.7389	11.19	16.1823
5	0.6118	-1.748	-0.2348	11.6425	4.1237	4.993	-0.0047	-0.1162	0.1322	0.6251	0.0632	-0.4029	0.2046	0.4309	-0.0584	0.1139	-0.0127	-0.0545	0.1735	0.0168	0.2142	27.1023	11.2726	35.2343
6	1.6342	0.5176	0.1023	1.8276	-0.0297	1.2838	0.0394	0.0197	0.0867	0.058	-0.066	-0.1983	-0.0835	0.1098	0.0267	0.0198	-0.0331	0.0008	0.0672	0.0173	0.099	18.6208	18.847	31.223
7	8.1674	3.0991	-1.5538	5.8643	0.8053	2.6221	-0.2162	0.0943	0.0251	-0.4085	0.0797	0.1202	-0.1101	0.0845	0.1365	0.0431	-0.0257	-0.0099	0.0296	0.0078	0.0665	13.7279	28.8449	26.0878
8	1.3217	1.4367	-0.7478	1.9128	-0.9436	1.8248	-0.0639	0.0068	-0.1296	-0.0794	-0.037	-0.1466	-0.0733	0.1105	0.1008	0.0147	-0.0052	0.0159	0.0586	0.0034	0.0863	13.0516	15.743	27.8005
9	1.685	0.1714	2.2826	7.289	-4.733	8.0598	0.1782	0.1302	-0.2929	-0.7167	0.0319	0.1916	0.5534	0.1531	-0.2102	0.2343	0.0505	-0.0033	0.1863	-0.0475	0.2099	15.8893	-7.0483	11.3
10	1.1751	-0.3275	0.2331	1.1625	0.0021	1.0747	0.0788	0.1101	-0.0585	-0.1115	-0.0293	-0.0818	0.1348	0.1257	-0.0495	0.0349	0.0353	0.0148	0.0761	-0.0149	0.111	16.3815	-4.7292	23.2889
11	5.7039	-0.4191	-1.8909	3.1861	-0.2963	3.0318	-0.0109	0.0612	0.1442	0.0219	-0.0408	-0.2587	-0.0117	0.1304	0.0517	0.0144	0.0259	-0.0102	0.064	0.0049	0.088	21.7691	-3.5119	34.3721
12	3.8814	0.0132	-0.0651	1.1326	-0.2104	0.3917	0.033	0.2645	-0.0831	-0.1054	-0.0337	-0.0721	0.0564	0.067	0.0007	0.0168	0.0185	0.0165	0.0746	-0.0008	0.0753	12.4957	1.2423	24.751

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 17
2	X-RAY DIFFRACTION	2	A	18 - 82
3	X-RAY DIFFRACTION	3	A	83 - 103
4	X-RAY DIFFRACTION	4	A	104 - 128
5	X-RAY DIFFRACTION	5	B	2 - 17
6	X-RAY DIFFRACTION	6	B	18 - 82
7	X-RAY DIFFRACTION	7	B	83 - 102
8	X-RAY DIFFRACTION	8	B	103 - 128
9	X-RAY DIFFRACTION	9	C	2 - 17
10	X-RAY DIFFRACTION	10	C	18 - 82
11	X-RAY DIFFRACTION	11	C	83 - 103
12	X-RAY DIFFRACTION	12	C	104 - 128

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