PDB-5v4d: Crystal Structure of the Protein of Unknown Function of the Conse...

ID or keywords:

Entry

Database: PDB / ID: 5v4d

Title

Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family YyfA from Yersinia pestis

Components

Putative translational inhibitor protein

Keywords

Structural genomics / unknown function / alpha-beta fold / enamine/imine demainase (Rid) / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

: / deaminase activity / hydrolase activity / metal ion binding / cytosol
Similarity search - Function

Biological species

Yersinia pestis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Kim, Y. / Chhor, G. / Endres, M. / Krishnan, A. / Babnigg, G. / Schneewind, O. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family YyfA from Yersinia pestis
Authors: Kim, Y. / Chhor, G. / Endres, M. / Krishnan, A. / Babnigg, G. / Schneewind, O. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Mar 9, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 5, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Jan 24, 2018	Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.3	Oct 4, 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 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5v4d.cif.gz	315.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5v4d.ent.gz	258 KB	Display	PDB format
PDBx/mmJSON format	5v4d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5v4d_validation.pdf.gz	488.5 KB	Display	wwPDB validaton report
Full document	5v4d_full_validation.pdf.gz	492.9 KB	Display
Data in XML	5v4d_validation.xml.gz	36.2 KB	Display
Data in CIF	5v4d_validation.cif.gz	53 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v4/5v4d ftp://data.pdbj.org/pub/pdb/validation_reports/v4/5v4d	HTTPS FTP

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Related structure data

Related structure data	1xrgS S: Starting model for refinement
Similar structure data	2b33-3 3r0p-1 2uyn-d 1pf5-1 1vd5-d 2uyj-d 3r0p-2 1xrg-d 5dc7-1 4wu0-2 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	TargetTrack: CSGID-IDP64152

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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) #4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Putative translational inhibitor protein

B: Putative translational inhibitor protein

C: Putative translational inhibitor protein

D: Putative translational inhibitor protein

E: Putative translational inhibitor protein

F: Putative translational inhibitor protein

hetero molecules

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

1

A: Putative translational inhibitor protein

B: Putative translational inhibitor protein

C: Putative translational inhibitor protein

hetero molecules

defined by author&software
Evidence: gel filtration
41.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Putative translational inhibitor protein

E: Putative translational inhibitor protein

F: Putative translational inhibitor protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	67.927, 80.919, 141.929
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Putative translational inhibitor protein Mass: 13709.498 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: tdcF3, y3551, YP_2944, YPO0627 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q7CGF7, UniProt: A0A3N4B564*PLUS
#2: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₄O₂
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 677 / 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: 2.37 Å³/Da / Density % sol: 48.12 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2 M calcium acetate, 0.1 M MES pH 6.0, 20 5(w/v) PEG8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 2, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 99444 / % possible obs: 96 % / Redundancy: 6.6 % / R_sym value: 0.081 / Net I/σ(I): 18.9
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3738 / CC_1/2: 0.795 / R_sym value: 0.505 / % possible all: 73.5

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2411)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDBID 1XRG

1xrg

Resolution: 1.6→41.958 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.85

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1796	4969	5 %	Random
R_work	0.1529	-	-	-
obs	0.1542	99374	95.83 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 22.3 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→41.958 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5727	0	52	677	6456

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	6124
X-RAY DIFFRACTION	f_angle_d	1.208	8371
X-RAY DIFFRACTION	f_dihedral_angle_d	13.704	3746
X-RAY DIFFRACTION	f_chiral_restr	0.084	1015
X-RAY DIFFRACTION	f_plane_restr	0.008	1108

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 (%)
1.6003-1.6185	0.2682	107	0.2292	2146	X-RAY DIFFRACTION	66
1.6185-1.6376	0.2637	133	0.2127	2574	X-RAY DIFFRACTION	80
1.6376-1.6575	0.2377	160	0.1971	2874	X-RAY DIFFRACTION	88
1.6575-1.6785	0.2476	167	0.1939	3086	X-RAY DIFFRACTION	96
1.6785-1.7006	0.2362	155	0.1791	3144	X-RAY DIFFRACTION	96
1.7006-1.7239	0.2408	156	0.1778	3143	X-RAY DIFFRACTION	97
1.7239-1.7485	0.2449	154	0.1609	3156	X-RAY DIFFRACTION	97
1.7485-1.7746	0.2218	159	0.1591	3184	X-RAY DIFFRACTION	97
1.7746-1.8024	0.2063	163	0.1588	3189	X-RAY DIFFRACTION	98
1.8024-1.8319	0.1983	175	0.1505	3147	X-RAY DIFFRACTION	97
1.8319-1.8635	0.2073	157	0.1537	3194	X-RAY DIFFRACTION	98
1.8635-1.8974	0.203	166	0.1513	3131	X-RAY DIFFRACTION	96
1.8974-1.9339	0.1908	165	0.1525	3115	X-RAY DIFFRACTION	96
1.9339-1.9733	0.1923	174	0.1546	3216	X-RAY DIFFRACTION	98
1.9733-2.0163	0.1867	177	0.1509	3174	X-RAY DIFFRACTION	98
2.0163-2.0632	0.1803	174	0.1372	3192	X-RAY DIFFRACTION	98
2.0632-2.1148	0.1823	170	0.1446	3233	X-RAY DIFFRACTION	98
2.1148-2.1719	0.1832	182	0.1457	3185	X-RAY DIFFRACTION	99
2.1719-2.2358	0.1897	161	0.1412	3242	X-RAY DIFFRACTION	99
2.2358-2.308	0.1726	171	0.1459	3125	X-RAY DIFFRACTION	95
2.308-2.3905	0.1828	160	0.1497	3245	X-RAY DIFFRACTION	99
2.3905-2.4862	0.2175	164	0.1527	3249	X-RAY DIFFRACTION	99
2.4862-2.5993	0.1797	167	0.1526	3273	X-RAY DIFFRACTION	99
2.5993-2.7363	0.1906	186	0.1589	3227	X-RAY DIFFRACTION	99
2.7363-2.9077	0.1862	183	0.1612	3266	X-RAY DIFFRACTION	99
2.9077-3.1322	0.1813	170	0.1578	3208	X-RAY DIFFRACTION	97
3.1322-3.4472	0.1883	185	0.1553	3302	X-RAY DIFFRACTION	99
3.4472-3.9457	0.151	178	0.1458	3346	X-RAY DIFFRACTION	100
3.9457-4.9699	0.1126	183	0.1296	3315	X-RAY DIFFRACTION	98
4.9699-41.9727	0.187	167	0.1645	3524	X-RAY DIFFRACTION	99

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	0.2825	0.0822	-0.1499	0.1793	0.2227	0.4805	0.182	0.0756	0.0035	-0.2069	0.1139	0.1311	0.1848	0.2193	0.0027	0.1959	-0.0047	-0.0193	0.188	-0.02	0.1834	34.7647	-5.0791	-24.8228
2	0.6272	0.0712	-0.1103	0.7048	0.2659	0.0284	0.0469	-0.0942	0.0448	-0.0079	0.0119	-0.0142	-0.0687	0.0369	0	0.141	-0.0157	-0.0025	0.1642	0.0019	0.1546	26.605	-5.2313	-15.8464
3	0.1895	0.3576	0.0632	0.445	0.002	0.0976	0.0232	-0.07	0.0187	-0.0179	-0.0385	0.0068	-0.0315	-0.0007	-0	0.1468	0.0045	0.0087	0.1537	0.0033	0.1616	19.1083	-7.4994	-13.6507
4	0.0542	0.0491	0.0505	0.0906	-0.0134	0.1513	-0.0646	0.201	-0.1625	-0.2156	0.0227	0.4488	0.0633	-0.2923	0.0005	0.1905	-0.0273	0.0195	0.2211	-0.0015	0.2372	12.0226	-17.1719	-43.0632
5	0.4742	0.4172	-0.0303	0.435	-0.3212	0.5066	0.0084	0.0443	-0.0445	-0.0844	0.0228	-0.0024	0.0256	0.0163	0	0.161	-0.0047	0.0095	0.1576	0.0047	0.1338	22.7651	-19.3132	-37.1765
6	0.0803	0.164	-0.2977	0.1599	0.0406	0.1475	0.0354	-0.0176	-0.0153	-0.0785	0.0004	-0.013	-0.0517	0.0489	-0	0.1657	-0.0098	0.0164	0.1688	0.0143	0.16	27.2807	-18.9624	-29.7485
7	0.5532	0.0281	0.2778	0.1472	-0.0792	0.2503	0.0074	-0.5266	0.103	0.0042	-0.0962	-0.0013	-0.1709	-0.1825	-0.025	0.1884	0.0077	-0.0049	0.2234	-0.0081	0.201	5.4645	0.0303	-16.3793
8	0.3818	-0.2307	0.0282	0.2189	0.0194	0.5963	0.0073	0.0841	0.0101	-0.0377	-0.0251	0.1317	-0.0182	-0.0779	0	0.1457	0.0048	-0.0076	0.1913	0.006	0.1773	2.0726	-12.0082	-26.0916
9	0.3875	-0.0516	0.0516	0.028	0.0738	0.2028	0.0343	0.0349	0.1037	-0.0251	-0.0278	0.0383	0.004	-0.0259	-0	0.1629	-0.0034	0.0014	0.164	0.0171	0.1484	9.0787	-15.0909	-23.0546
10	0.5257	-0.122	-0.1742	0.1473	0.2173	0.6028	-0.0894	-0.1385	0.0128	0.1656	0.0748	0.0564	0.1578	0.1085	-0.0002	0.1947	0.026	-0	0.1667	0.0133	0.1836	31.8894	-48.2379	4.0637
11	0.0333	0.0229	0.0667	0.0818	0.0059	0.0778	-0.1593	0.0391	0.0381	-0.1163	-0.0053	-0.1225	-0.1379	0.1137	-0.0017	0.1961	-0.0145	-0.0359	0.2077	-0.0076	0.1848	43.0595	-34.3893	-2.6458
12	0.1787	0.0124	0.1526	0.0369	-0.0267	0.0726	0.1287	0.044	0.0268	-0.0362	-0.2261	-0.1417	0.0905	0.4729	-0.0004	0.1591	0.0375	-0.0047	0.2097	0.0073	0.1802	41.0401	-44.4061	-6.1347
13	0.2746	-0.1909	0.178	0.335	0.1468	0.4476	0.0091	0.0828	-0.0162	-0.0026	-0.0021	-0.0086	0.059	0.0917	0	0.1441	0.0149	0.0101	0.1419	-0.004	0.1446	34.1948	-45.3669	-13.0854
14	0.0644	0.0377	0.0364	0.0218	-0.0227	0.0798	-0.0073	-0.0753	0.0031	0.2675	0.0262	0.2032	-0.0951	0.0955	0.0004	0.1614	0.0179	0.024	0.1283	0.0196	0.1811	30.6121	-49.9987	-5.6326
15	0.1517	0.025	-0.0443	0.1886	0.1873	0.3708	0.0865	0.061	0.0243	-0.1442	-0.1424	-0.098	0.0663	-0.1903	-0.0004	0.236	-0.0056	0.0501	0.1797	-0.0118	0.1852	7.3501	-51.5893	-2.5951
16	0.3453	-0.0314	-0.1022	0.1097	-0.0741	0.4242	0.0199	-0.0676	0.0549	-0.0132	-0.0402	0.0346	0.0327	-0.0203	-0	0.1491	-0.0029	0.0108	0.1511	-0.003	0.1578	14.1999	-37.9184	4.4739
17	0.3167	-0.0288	0.028	0.164	0.0711	0.3517	0.0034	0.0392	0.003	-0.009	-0.0355	0.0644	0.0851	0.0211	-0.0003	0.1652	0.0059	-0.0053	0.1361	0.0111	0.1554	19.0537	-39.9412	-0.1818
18	0.0369	0.0605	0.1012	0.0492	0.0452	0.1016	0.0711	0.2862	-0.1452	0.1006	0.0148	-0.106	-0.0656	0.3581	0	0.2426	-0.0065	-0.0068	0.2151	-0.0142	0.1866	27.9011	-57.3599	-22.2773
19	0.4872	0.1233	-0.2131	0.6672	0.3785	0.611	0.0169	0.0742	-0.0601	-0.0214	-0.0558	0.0449	0.1196	-0.1016	-0	0.1686	-0.0219	0.0002	0.1492	-0.0062	0.1468	15.0147	-49.4814	-20.6904
20	0.0827	-0.0136	-0.0218	0.0511	-0.0023	0.0429	0.1578	-0.2296	-0.098	-0.2032	0.0053	0.1041	-0.0174	-0.4928	0.0071	0.2537	-0.0867	-0.0151	0.2891	-0.0444	0.2283	4.2614	-53.7612	-13.6462
21	0.2153	0.1168	-0.0035	0.0926	0.1173	0.1213	0.0447	0.0226	-0.0212	0.0426	-0.0301	0.0434	0.0357	-0.0125	0	0.1586	-0.0061	0.0134	0.1464	0.01	0.1524	18.3198	-43.6909	-16.1082

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 19 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 20 through 81 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 82 through 126 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 19 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 20 through 81 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 82 through 126 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 19 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 20 through 102 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 103 through 126 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 0 through 34 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 35 through 46 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 47 through 64 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 65 through 117 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 118 through 126 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 0 through 29 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 30 through 96 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 97 through 126 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 1 through 19 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 20 through 95 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 96 through 102 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 103 through 126 )

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