PDB-4m20: Crystal Structure of hypothetical protein SAV0944 from Staphyloco...

ID or keywords:

Entry

Database: PDB / ID: 4m20

Title

Crystal Structure of hypothetical protein SAV0944 from Staphylococcus aureus subsp. aureus Mu50

Components

Uncharacterized protein

Keywords

HYDROLASE / Thioesterase / Hot Dog Fold / hydrolysis of thioester bond

Function / homology

Function and homology information

1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / phylloquinone biosynthetic process / menaquinone biosynthetic process / peroxisome / cytosol
Similarity search - Function

Biological species

Staphylococcus aureus subsp. aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Khandokar, Y.B. / Forwood, J.K.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Expression, purification, crystallization and preliminary X-ray analysis of the PaaI-like thioesterase SAV0944 from Staphylococcus aureus.
Authors: Khandokar, Y.B. / Roman, N. / Smith, K.M. / Srivastava, P. / Forwood, J.K.

History

Deposition	Aug 5, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 1, 2014	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 20, 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 / 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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Download

PDBx/mmCIF format	4m20.cif.gz	205.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4m20.ent.gz	166.2 KB	Display	PDB format
PDBx/mmJSON format	4m20.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4m20_validation.pdf.gz	1022.7 KB	Display	wwPDB validaton report
Full document	4m20_full_validation.pdf.gz	1 MB	Display
Data in XML	4m20_validation.xml.gz	23.6 KB	Display
Data in CIF	4m20_validation.cif.gz	31.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m2/4m20 ftp://data.pdbj.org/pub/pdb/validation_reports/m2/4m20	HTTPS FTP

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Related structure data

Related structure data	1sbkS S: Starting model for refinement
Similar structure data	4ybv-d 2jgs-d 3tnz-d 6ica-2 3csj-d 5ep5-d 1efz-d 3nxl-3 1tw9-3 2ofb-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

hetero molecules

56.9 kDa, 4 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)	44.050, 89.050, 60.740
Angle α, β, γ (deg.)	90.00, 100.53, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
3	1	chain C
4	1	chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	THR	THR	PRO	PRO	chain A	A	A	2 - 122	5 - 125
2	HIS	HIS	LEU	LEU	chain B	B	B	3 - 123	6 - 126
3	HIS	HIS	LEU	LEU	chain C	C	C	3 - 123	6 - 126
4	HIS	HIS	PRO	PRO	chain D	D	D	3 - 122	6 - 125

#1: Protein	Uncharacterized protein Mass: 13836.954 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: Mu50 / Gene: SAV0944 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PlysS / References: UniProt: Q99VD7, UniProt: A0A0H3JUJ1*PLUS
#2: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.12 Å³/Da / Density % sol: 41.88 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 24%PEG4000, 100mM sodium citrate pH6.5, and 12%2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2013
Radiation	Monochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2→30.145 Å / Num. obs: 30924 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2→2.05 Å / % possible all: 99.4

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Processing

Software

Name	Version	Classification
Blu-Ice	(McPhillips	data collection
CCP4		model building
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
MOSFLM		data reduction
SCALA		data scaling
CCP4		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1SBK

1sbk

Resolution: 2→30.145 Å / SU ML: 0.25 / σ(F): 1.93 / Phase error: 23.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2204	1559	5.05 %	RANDOM
R_work	0.1735	-	-	-
obs	0.1759	30901	99.17 %	-
all	-	31160	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2→30.145 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3687	0	96	192	3975

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3860
X-RAY DIFFRACTION	f_angle_d	1.298	5235
X-RAY DIFFRACTION	f_dihedral_angle_d	15.147	1399
X-RAY DIFFRACTION	f_chiral_restr	0.058	617
X-RAY DIFFRACTION	f_plane_restr	0.007	647

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	2224	X-RAY DIFFRACTION	POSITIONAL	7.533
1	2	B	2224	X-RAY DIFFRACTION	POSITIONAL	7.533
1	3	C	2224	X-RAY DIFFRACTION	POSITIONAL	7.533
1	4	D	2224	X-RAY DIFFRACTION	POSITIONAL	7.533

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 (%)
2.0001-2.0646	0.2819	128	0.2369	2669	X-RAY DIFFRACTION	99
2.0646-2.1384	0.2825	140	0.2227	2645	X-RAY DIFFRACTION	99
2.1384-2.224	0.2482	140	0.1956	2658	X-RAY DIFFRACTION	99
2.224-2.3252	0.2704	137	0.2055	2687	X-RAY DIFFRACTION	99
2.3252-2.4477	0.2821	155	0.2019	2649	X-RAY DIFFRACTION	99
2.4477-2.601	0.2802	128	0.2022	2661	X-RAY DIFFRACTION	99
2.601-2.8017	0.2334	132	0.1894	2667	X-RAY DIFFRACTION	99
2.8017-3.0834	0.2442	162	0.1863	2653	X-RAY DIFFRACTION	99
3.0834-3.529	0.2134	140	0.1691	2680	X-RAY DIFFRACTION	100
3.529-4.4439	0.1736	144	0.1365	2694	X-RAY DIFFRACTION	99
4.4439-30.4183	0.197	153	0.1597	2679	X-RAY DIFFRACTION	98

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	3.6813	-1.9097	0.5669	2.809	-0.7207	0.9316	0.1608	0.414	0.0804	-0.263	0.0051	0.114	-0.1085	0.1737	-0.2059	0.233	0.0275	0.0213	0.3414	0.0467	0.3532	20.8223	33.3838	-2.0688
2	3.5734	-1.2774	0.7238	3.2301	-1.2982	1.8955	-0.0103	-0.1265	1.0104	0.1666	-0.162	0.1556	-0.3615	0.0523	0.1872	0.222	-0.0257	-0.0073	0.2143	-0.0669	0.682	13.4278	41.4397	6.2045
3	1.481	-0.1214	-0.1654	1.2468	-0.1465	0.7987	-0.0519	0.2968	-0.0795	-0.1901	-0.1584	-0.1005	0.1295	0.1871	0.1845	0.1983	0.01	0.0287	0.3308	0.0214	0.2531	16.4359	23.224	2.6668
4	1.3154	0.1604	-0.1294	2.7641	-0.0377	1.8689	0.0208	-0.183	0.336	0.2531	-0.018	-0.2782	0.0007	0.1616	0.0185	0.0938	-0.0046	-0.0169	0.2681	-0.0122	0.31	19.567	28.7308	10.0099
5	6.0596	1.154	0.4218	3.4113	0.2883	3.9337	-0.3949	0.0702	0.5405	-0.1002	0.0159	0.1139	-0.3898	0.0001	0.1693	0.2458	0.0177	0.0256	0.2185	0.1066	0.4186	2.5987	41.393	-0.2771
6	1.3869	-0.1943	-1.1859	0.6271	-0.1747	1.7058	0.2029	0.2231	0.3797	-0.0137	0.012	0.3602	-0.1388	-0.1127	-0.1003	0.1501	0.0187	0.0553	0.2233	0.0525	0.3075	-8.5379	35.5395	5.8133
7	5.3188	2.146	0.9673	1.1947	-0.7782	4.411	0.0604	0.7474	-0.2227	-0.4572	-0.1344	-0.1079	0.4598	0.2294	0.0109	0.2722	0.0896	0.0363	0.4016	0.0523	0.2362	8.2171	29.0515	-6.9668
8	1.044	-0.5838	-0.4216	1.0426	0.0895	0.9158	0.0236	-0.1194	0.0945	0.2198	0.0318	0.128	-0.1827	0.078	-0.0248	0.2191	-0.0124	0.0654	0.1938	-0.0308	0.2332	1.0755	36.0433	13.9111
9	1.037	-1.9994	2.7796	5.0122	-5.3882	7.4656	-0.0989	0.3024	0.0463	-0.6059	-0.1	-0.1	0.3739	0.0916	0.0404	0.4055	0.0415	-0.0476	0.4906	-0.0339	0.2354	1.8564	22.3401	-5.0454
10	1.4288	0.3261	-0.652	1.5796	-0.0255	7.1719	0.0782	0.0502	0.1492	0.159	-0.055	0.357	0.1438	-0.2126	0.0456	0.1268	-0.0019	0.0462	0.1883	0.0371	0.2763	-6.0495	30.0516	11.2463
11	1.5908	-0.2817	0.1777	2.5519	2.9278	2.03	0.026	-0.0666	0.1177	0.2588	-0.061	0.1921	0.1573	-0.1553	-0.0684	0.212	-0.0416	0.0692	0.1852	-0.0111	0.2586	-2.8001	30.1255	16.1223
12	7.4309	2.7891	1.8886	8.5988	-4.4455	2.0031	0.0845	0.5678	0.0801	-0.4899	0.0299	0.1585	0.0616	-0.2043	-0.0756	0.3054	-0.076	0.0206	0.4908	-0.0258	0.3618	-6.0393	22.1351	-3.953
13	1.3281	-0.5285	-0.4716	2.0716	0.1963	1.5273	0.0548	0.0955	0.3327	0.1758	0.0468	-0.0237	-0.1616	0.1482	-0.1334	0.1384	-0.0121	-0.006	0.1328	0.0091	0.221	1.8069	31.1242	15.309
14	0.8577	-0.1712	0.1225	0.3779	0.0101	2.0634	-0.0859	0.0265	-0.7861	1.0958	-0.2755	0.7009	0.6176	0.107	0.1175	0.8827	-0.0266	0.1221	0.1153	0.2689	0.1791	-1.1686	5.5643	27.7522
15	0.2664	0.7624	1.01	2.1538	2.7765	4.1803	-0.0166	-0.5815	0.6992	0.2978	-0.0054	-0.1634	-0.4956	0.201	-0.0226	1.3003	0.127	-0.1692	0.6053	0.0519	-0.1022	5.5538	19.2585	37.8467
16	0.9461	0.4828	1.0213	1.0093	1.8413	3.2809	0.0083	0.0104	-0.0748	0.4968	0.0475	0.0475	-0.0585	0.1321	-0.0116	0.3646	-0.0211	0.0065	0.1881	0.0398	0.2332	2.6193	8.3294	20.2279
17	1.4837	0.4536	0.3521	0.8355	-0.5337	0.5194	0.034	-0.0453	-0.1323	0.4261	0.1378	0.1597	0.0097	-0.0396	-0.1676	0.3308	-0.0037	0.0177	0.2241	0.0237	0.2182	1.6924	11.2206	18.9487
18	3.1325	0.2195	-1.7579	1.9472	0.5341	7.9702	0.3075	0.2728	0.0115	0.0012	0.0132	0.2035	-0.3549	-0.2111	-0.215	0.2549	-0.0491	-0.0351	0.1721	0.0423	0.2669	0.2141	12.5644	13.3393
19	9.6657	0.8491	-0.9717	6.4547	1.148	2.0014	-0.0717	-0.1104	-0.075	0.0545	0.008	0.2497	0.1333	-0.2235	0.0275	0.5665	0.2118	0.1671	0.555	0.0678	0.4931	-10.1822	18.5376	31.65
20	1.2832	0.2259	-0.1905	2.6019	0.4283	1.9833	0.0157	0.0519	0.0047	0.2234	0.0834	-0.1558	-0.0985	0.1382	-0.1333	0.2596	-0.0472	-0.0332	0.1992	0.0011	0.2086	4.8562	12.2212	15.606
21	1.1156	0.693	0.0618	1.8097	0.0664	0.7759	-0.082	-0.9422	-0.1493	0.7951	0.3725	-0.205	0.3784	0.8509	-0.0063	0.8568	0.3208	-0.583	0.6262	0.2037	-0.6809	19.1456	13.9064	34.5066
22	0.3107	-1.0136	-0.4593	3.228	1.4808	0.6812	-0.1476	0.5628	-0.9187	-0.4602	-0.239	0.1991	0.5937	-0.2828	0.1516	0.8494	0.1201	0.0683	0.4574	0.0979	0.7155	12.367	1.5543	22.3966
23	1.0645	0.6748	0.5393	2.4732	0.9513	1.2503	0.0593	-0.6679	-0.1137	0.6613	-0.0092	0.0087	-0.3958	0.223	-0.1086	0.8209	0.0245	-0.0696	0.5507	-0.0532	0.1615	14.0161	24.6052	34.1905
24	0.4566	-0.318	-0.1937	1.3334	1.2321	1.1667	0.0183	-0.3736	0.1133	0.3982	0.0267	-0.0627	-0.1649	0.0356	0.0587	0.4701	-0.0142	-0.0264	0.3138	-0.0369	0.2176	9.8213	22.6865	24.757
25	1.8815	-0.764	0.2246	1.4266	-0.8869	1.6772	-0.1011	-0.5967	-0.0906	0.4388	0.3281	-0.5124	0.2542	0.5521	-0.0894	0.4029	0.0714	-0.1235	0.5981	-0.0022	0.2932	21.3251	16.7554	24.7285
26	2.0306	-1.2433	-0.1041	5.8046	-0.3724	1.8224	0.643	-0.1414	0.5044	0.1018	0.223	-0.3412	-0.293	0.3342	-0.261	0.498	-0.0736	-0.281	0.4591	-0.2261	0.2221	17.2429	26.9669	25.9142
27	7.4894	-0.4883	-3.104	2.0021	-1.1483	1.4538	-0.1503	-0.1058	-0.1169	0.2436	-0.1183	-0.2954	0.0034	0.3134	0.0756	0.4889	-0.023	-0.2201	0.6002	-0.0508	0.6574	27.8301	8.1087	22.0262
28	0.9842	-0.0864	0.2289	2.6475	0.6677	2.183	0.1479	-0.3074	0.0436	0.222	-0.2323	0.166	-0.1416	-0.0796	0.0911	0.4598	-0.0183	-0.0629	0.3982	-0.1148	0.2312	13.2557	24.0499	25.3052

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 18 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 74 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 75 through 122 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 3 through 10 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 11 through 25 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 26 through 38 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 39 through 74 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 75 through 81 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 82 through 92 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 93 through 104 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 105 through 109 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 110 through 123 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 3 through 30 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 31 through 38 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 39 through 57 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 58 through 92 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 93 through 104 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 105 through 109 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 110 through 123 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 3 through 30 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 31 through 38 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 39 through 63 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 64 through 74 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 75 through 92 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 93 through 104 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 105 through 109 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 110 through 122 )

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About Yorodumi

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Yorodumi