PDB-4d3h: Structure of PstA

ID or keywords:

Entry

Database: PDB / ID: 4d3h

Title

Structure of PstA

Components

PSTA

Keywords

SIGNALLING PROTEIN / GRAM-POSITIVE / C-DI-AMP

Function / homology

Function and homology information

Cyclic-di-AMP receptor / Cyclic-di-AMP receptor / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

STAPHYLOCOCCUS AUREUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Campeotto, I. / Freemont, P. / Grundling, A.

Citation

Journal: J.Biol.Chem. / Year: 2015
Title: Complex Structure and Biochemical Characterization of the Staphylococcus Aureus Cyclic Di-AMP Binding Protein Psta, the Founding Member of a New Signal Transduction Protein Family
Authors: Campeotto, I. / Zhang, Y. / Mladenov, M.G. / Freemont, P.S. / Grundling, A.

History

Deposition	Oct 22, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 24, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 31, 2014	Group: Database references
Revision 1.2	Feb 11, 2015	Group: Database references
Revision 1.3	Sep 13, 2017	Group: Data collection / Category: diffrn_detector / diffrn_source Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_sheet / struct_site Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4d3h.cif.gz	139.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4d3h.ent.gz	109.8 KB	Display	PDB format
PDBx/mmJSON format	4d3h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4d3h_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	4d3h_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4d3h_validation.xml.gz	16 KB	Display
Data in CIF	4d3h_validation.cif.gz	21.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d3/4d3h ftp://data.pdbj.org/pub/pdb/validation_reports/d3/4d3h	HTTPS FTP

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Related structure data

Related structure data	4d3gC 4drg PDB Unreleased entryS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2j9d-4 1w58-d 4gs0-1 1w5e-3 5u2c-d 1w5e-4 1w5e-1 1w5e-8 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PSTA

B: PSTA

C: PSTA

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	64.206, 65.655, 85.156
Angle α, β, γ (deg.)	90.00, 95.98, 90.00
Int Tables number	5
Space group name H-M	I121

Components on special symmetry positions

ID	Model	Components
1	1	A-2008- HOH
2	1	A-2048- HOH

#1: Protein	PSTA Mass: 13886.558 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99WC0, UniProt: Q2G229*PLUS
#2: Chemical	ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate Mass: 658.412 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₀H₂₄N₁₀O₁₂P₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 169 / 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: 42.69 % / Description: NONE
Crystal grow	pH: 4.6 / Details: 200MM NA MALONATE PH=4.6, 20% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2→42.35 Å / Num. obs: 23649 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / R_merge(I) obs: 0.08 / Net I/σ(I): 9.6
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DRG

4drg
PDB Unreleased entry

Resolution: 2→53.75 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.928 / SU B: 7.067 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23176	1315	5.6 %	RANDOM
R_work	0.18805	-	-	-
obs	0.19056	22328	98.85 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 25.963 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.19 Å²	0 Å²	-0.12 Å²
2-	-	0.82 Å²	0 Å²
3-	-	-	-0.96 Å²

Refinement step

Cycle: LAST / Resolution: 2→53.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2342	0	132	169	2643

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	2520
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	2357
X-RAY DIFFRACTION	r_angle_refined_deg	1.823	2.018	3438
X-RAY DIFFRACTION	r_angle_other_deg	1.312	3	5397
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.758	5	302
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.999	25.221	113
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.776	15	400
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.687	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	404
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2823
X-RAY DIFFRACTION	r_gen_planes_other	0.004	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	1.648	1.764	1226
X-RAY DIFFRACTION	r_mcbond_other	1.648	1.764	1225
X-RAY DIFFRACTION	r_mcangle_it	2.599	2.623	1522
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.396	2.08	1294
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	89	-
R_work	0.236	1647	-
obs	-	-	99.77 %

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	0.8072	-1.9447	-0.3869	4.7314	1.113	3.0987	0.1464	0.0076	-0.0449	-0.3013	-0.0357	0.0925	-0.1802	0.159	-0.1107	0.1013	-0.0353	-0.0065	0.0616	0.0092	0.0155	5.9006	-7.6482	0.5703
2	1.9918	2.627	4.0323	3.8321	4.9951	8.4577	-0.004	-0.0855	0.0474	-0.0058	-0.0855	0.0933	-0.0257	-0.1938	0.0895	0.0293	0.0024	-0.0159	0.0538	-0.0163	0.0654	4.0093	-17.7741	-14.95
3	1.264	-0.7233	-0.9377	1.2424	2.7233	9.0906	-0.0487	0.0285	-0.1619	0.0178	-0.1156	0.1297	0.0321	-0.2963	0.1642	0.0271	-0.0332	0.013	0.0635	-0.0072	0.0435	-8.4491	-24.4662	-15.9138
4	0.513	0.213	-1.3914	0.9229	-1.7628	5.4575	0.0904	-0.1703	-0.1303	-0.0653	0.0762	0.3175	-0.0813	0.2675	-0.1666	0.0371	-0.0551	-0.0563	0.0988	0.094	0.2055	-5.1004	-15.6542	-14.8836
5	0.2333	-0.0912	-0.6238	1.1128	1.8379	4.157	-0.0661	0.0334	0.0137	-0.026	0.0031	0.0514	0.0312	-0.1145	0.0629	0.0634	0.0087	-0.0259	0.0393	-0.0049	0.0445	0.6456	-19.9354	-26.4895
6	1.221	1.5593	2.4216	4.7872	5.1923	6.4169	-0.0749	0.0185	-0.1152	0.2379	0.0542	0.2066	0.1362	0.0563	0.0207	0.0871	-0.0195	0.036	0.026	0.0032	0.0619	0.5189	-26.4141	-10.825
7	6.5023	0.9943	2.7569	6.5105	2.1305	1.6291	0.0628	0.1991	-0.3166	0.0657	0.0871	-0.0976	0.0385	0.1052	-0.1499	0.0184	-0.0134	-0.0079	0.0421	-0.0333	0.0523	-5.1317	-42.2557	-29.0071
8	0.8087	0.3444	0.1446	2.8465	0.9359	0.3165	0.0548	0.0671	-0.0449	0.0308	-0.0115	-0.083	-0.0103	-0.0038	-0.0434	0.1035	-0.002	0.0251	0.0336	0.0051	0.0197	4.1698	-14.7072	-13.291
9	4.859	1.9479	-2.8928	0.7957	-0.8775	7.5314	-0.1002	0.0436	-0.152	-0.0301	0.0069	-0.0573	0.1213	-0.149	0.0932	0.0602	-0.0139	-0.0095	0.0107	-0.0104	0.0607	22.6795	0.4771	-18.2934
10	8.9009	0.0021	1.5493	0.2352	0.157	0.376	0.0125	0.0215	0.1202	0.0381	-0.0187	-0.015	0.0185	-0.0132	0.0062	0.0596	0.0066	0.0064	0.0469	0.0185	0.0287	2.4048	-3.775	-16.507
11	6.7418	4.7222	-1.1765	5.0447	-0.9527	0.2768	0.0512	0.0795	0.1673	0.0497	0.0318	0.1643	-0.0866	-0.0556	-0.083	0.1032	0.0504	0.0515	0.0333	0.0407	0.0589	-2.8482	6.9826	-21.2383
12	1.4629	1.0435	-1.4613	0.7466	-1.0394	1.4643	-0.0424	0.1183	0.0117	-0.0216	0.0784	-0.0029	0.038	-0.1223	-0.036	0.0777	0.0385	0.0198	0.0471	0.0349	0.0877	1.6738	-1.4491	-24.1524
13	4.7696	1.9223	-0.126	1.1257	-0.7454	1.3813	-0.0232	0.2619	0.111	0.0182	0.1819	0.123	-0.0647	-0.1609	-0.1586	0.0435	0.0313	0.0058	0.054	0.0179	0.0243	-5.6658	-8.3836	-18.3421
14	7.1346	0.5569	-0.0499	0.1141	0.0789	0.672	0.0667	-0.0196	0.0413	0.0398	-0.0117	0.0183	-0.1872	-0.0125	-0.055	0.109	-0.0019	0.0351	0.007	-0.0018	0.0266	3.4404	4.9885	-12.4784
15	7.5152	4.9346	1.1044	3.2417	0.7265	4.2861	0.5902	-0.2815	-0.0773	0.385	-0.1805	-0.0415	-0.0901	0.0764	-0.4097	0.0641	-0.0132	0.0177	0.0401	0.0232	0.111	-22.8177	-1.6118	-8.3238
16	1.3334	-0.822	-0.3487	0.5368	0.3578	0.9369	0.0251	-0.0374	-0.1177	-0.0342	0.0224	0.0503	-0.2228	0.0085	-0.0475	0.1087	-0.0044	0.0003	0.0112	0.0048	0.0432	8.1714	-4.6881	-17.7496
17	6.9266	3.7234	2.4187	2.5605	2.1274	2.3761	-0.199	-0.0753	-0.0676	-0.1098	0.1827	0.104	-0.0001	0.1275	0.0163	0.0272	-0.0302	-0.0455	0.1834	0.1406	0.1464	18.1647	-27.7088	-14.27
18	1.2199	-0.3294	-0.0559	0.5647	-0.9874	2.3834	0.0033	0.0912	0.0307	-0.0668	-0.0541	-0.0601	0.0221	0.0931	0.0508	0.0881	-0.0005	0.0117	0.0293	-0.0117	0.0319	12.5956	-14.7277	-32.283
19	0.7121	-1.2109	-0.1714	5.46	0.0118	1.1086	0.0364	0.1489	-0.09	-0.0404	-0.0272	0.3268	0.0041	-0.1125	-0.0092	0.0393	0.0026	-0.0064	0.0502	-0.006	0.0207	3.8488	-9.0588	-30.3129
20	3.5407	-4.7695	2.7945	6.4399	-3.8418	3.0157	0.0196	0.0417	-0.007	-0.0216	-0.0284	-0.0037	-0.0442	-0.0461	0.0089	0.0458	-0.0267	-0.0223	0.0739	-0.0072	0.0452	5.7377	-9.1047	-29.4427
21	2.9173	-0.8667	2.7028	4.038	-4.7929	6.7609	-0.0885	-0.0034	-0.133	-0.1618	-0.0916	-0.2982	0.0658	0.0827	0.1801	0.0739	0.0238	0.0744	0.0278	0.0077	0.0977	20.447	-14.9212	-29.9954
22	1.0486	-4.203	0.5607	20.0062	-3.1896	0.5901	0.076	-0.1078	0.0654	-0.6492	-0.0564	-0.0429	0.1278	0.0584	-0.0196	0.1338	0.0747	-0.0385	0.1872	-0.0749	0.032	14.7754	-2.1461	-40.3138
23	1.8286	-4.424	-0.3154	10.7358	0.6417	0.5446	0.1637	0.0309	-0.2067	-0.2952	-0.1105	0.5152	-0.4401	0.101	-0.0532	0.3613	-0.0823	0.0593	0.0588	0.0033	0.0588	7.0835	7.4869	-38.2659
24	0.3283	0.2753	0.2591	1.63	-1.1854	1.6183	-0.0161	0.0185	-0.0304	0.0935	0.0202	-0.0286	-0.1226	0.0007	-0.0042	0.0549	0.0313	0.0164	0.0273	-0.0053	0.0609	11.8083	-14.6328	-21.6753

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-8 - 0
2	X-RAY DIFFRACTION	2	A	1 - 8
3	X-RAY DIFFRACTION	3	A	9 - 24
4	X-RAY DIFFRACTION	4	A	25 - 30
5	X-RAY DIFFRACTION	5	A	31 - 48
6	X-RAY DIFFRACTION	6	A	49 - 67
7	X-RAY DIFFRACTION	7	A	68 - 92
8	X-RAY DIFFRACTION	8	A	93 - 109
9	X-RAY DIFFRACTION	9	B	-7 - 0
10	X-RAY DIFFRACTION	10	B	1 - 10
11	X-RAY DIFFRACTION	11	B	11 - 24
12	X-RAY DIFFRACTION	12	B	25 - 32
13	X-RAY DIFFRACTION	13	B	33 - 48
14	X-RAY DIFFRACTION	14	B	49 - 66
15	X-RAY DIFFRACTION	15	B	67 - 92
16	X-RAY DIFFRACTION	16	B	93 - 109
17	X-RAY DIFFRACTION	17	C	-8 - -1
18	X-RAY DIFFRACTION	18	C	0 - 25
19	X-RAY DIFFRACTION	19	C	26 - 37
20	X-RAY DIFFRACTION	20	C	38 - 48
21	X-RAY DIFFRACTION	21	C	49 - 63
22	X-RAY DIFFRACTION	22	C	64 - 69
23	X-RAY DIFFRACTION	23	C	70 - 92
24	X-RAY DIFFRACTION	24	C	93 - 109

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