PDB-3qbo: Crystal structure of phosphoserine aminotransferase from Yersinia...

ID or keywords:

Entry

Database: PDB / ID: 3qbo

Title

Crystal structure of phosphoserine aminotransferase from Yersinia pestis CO92

Components

Phosphoserine aminotransferase

Keywords

TRANSFERASE / SerC / 3-phosphoserine aminotransferase / PSAT / PLP binding / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / biosynthesis of the coenzyme pyridoxal 5'-phosphate / phosphorylated pathway of serine biosynthesis

Function / homology

Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta / PYRIDOXAL-5'-PHOSPHATE

Function and homology information

Biological species

Yersinia pestis CO92 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.36 Å

Authors

Nocek, B. / Maltseva, N. / Papazisi, L. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of phosphoserine aminotransferase from Yersinia pestis CO92
Authors: Nocek, B. / Maltseva, N. / Papazisi, L. / Anderson, W. / Joachimiak, A.

History

Deposition	Jan 13, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 9, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3qbo.cif.gz	289.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3qbo.ent.gz	248.5 KB	Display	PDB format
PDBx/mmJSON format	3qbo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3qbo_validation.pdf.gz	456.8 KB	Display	wwPDB validaton report
Full document	3qbo_full_validation.pdf.gz	466.9 KB	Display
Data in XML	3qbo_validation.xml.gz	29.4 KB	Display
Data in CIF	3qbo_validation.cif.gz	41.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qb/3qbo ftp://data.pdbj.org/pub/pdb/validation_reports/qb/3qbo	HTTPS FTP

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Related structure data

Similar structure data	2c0r-d 3ly7-1 4azk-d 2bi2-d 3ffr-1 5f8v-2 2ww3-3 5yb0-2 2ww1-4 4w91-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: idp90566

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phosphoserine aminotransferase

B: Phosphoserine aminotransferase

hetero molecules

81.2 kDa, 2 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)	78.338, 87.951, 106.177
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Phosphoserine aminotransferase Mass: 40330.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: phosphoserine transaminase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H₂O
Nonpolymer details	The aldehyde group of PLP forms a Schiff-base linkage (internal aldimine) with the side-chain amino ...The aldehyde group of PLP forms a Schiff-base linkage (internal aldimine) with the side-chain amino group of the lysine

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.75 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.8 Potassium Sodium tartrate tetrahydrate 0.5 PEGME 5000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2010 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.35→40 Å / Num. all: 30934 / Num. obs: 30628 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / B_iso Wilson estimate: 42.1 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 12
Reflection shell	Resolution: 2.35→2.39 Å / % possible all: 98.9

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
MOLREP		phasing
REFMAC	5.5.0109	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.36→40 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.903 / SU B: 17.597 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26107	1534	5 %	RANDOM
R_work	0.19673	-	-	-
all	0.2	30591	-	-
obs	0.20012	29057	98.96 %	-

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: 26.279 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1 Å²	0 Å²	0 Å²
2-	-	-1.75 Å²	0 Å²
3-	-	-	2.75 Å²

Refinement step

Cycle: LAST / Resolution: 2.36→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5586	0	30	185	5801

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	5744
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3843
X-RAY DIFFRACTION	r_angle_refined_deg	1.611	1.954	7786
X-RAY DIFFRACTION	r_angle_other_deg	0.977	3	9343
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.963	5	715
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.113	24.244	271
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.408	15	941
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.054	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	836
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	6478
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1176
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	0.85	1.5	3560
X-RAY DIFFRACTION	r_mcbond_other	0.158	1.5	1459
X-RAY DIFFRACTION	r_mcangle_it	1.576	2	5686
X-RAY DIFFRACTION	r_scbond_it	2.395	3	2184
X-RAY DIFFRACTION	r_scangle_it	3.892	4.5	2100
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.358→2.419 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.298	77	-
R_work	0.225	1962	-
obs	-	-	91.19 %

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	-0.5197	-0.6588	-0.6555	3.7448	1.0602	-0.6129	0.0418	-0.0301	-0.0297	-0.2477	-0.0851	0.0574	-0.0253	0.057	0.0432	0.1674	-0.0062	0.0074	0.1648	-0.0324	0.109	55.878	74.577	-0.866
2	-0.0187	0.8667	-0.6147	8.159	-1.1197	0.5821	-0.1919	-0.1232	0.1485	-0.4772	0.0715	0.4431	0.0071	0.1385	0.1204	0.128	-0.0222	-0.0473	0.137	-0.0245	0.1467	52.358	93.998	-3.204
3	10.5333	6.7707	10.2996	19.1412	1.5749	7.9981	0.1589	-0.1284	0.4941	0.1681	-0.378	0.9839	0.0047	0.078	0.2191	0.1651	0.0535	0.0743	0.081	-0.0542	0.1251	46.036	98.469	7.964
4	0.1622	0.0323	0.3608	1.4301	0.0677	0.8713	0.0445	-0.0138	0.0544	0.1962	-0.1417	0.1881	-0.0853	0.0386	0.0972	0.1393	-0.0375	0.0506	0.1479	-0.031	0.0745	46.956	80.634	22.009
5	-0.1667	0.5334	1.1934	4.9459	1.9416	2.122	0.3087	-0.0062	-0.191	0.6574	-0.3616	-0.3098	0.2549	0.154	0.053	0.2322	-0.1054	-0.0596	0.1114	0.1105	0.0809	54.933	64.63	29.368
6	0.4619	-0.373	-1.5593	1.7254	1.3746	2.492	0.0811	-0.0132	-0.0881	0.2723	-0.0611	0.0446	0.1083	0.1522	-0.02	0.2083	-0.0208	0.0213	0.1299	-0.0057	0.1198	49.022	66.797	24.515
7	-0.0138	0.0201	0.1109	0.582	0.3994	1.0182	0.0317	0.0146	-0.1058	0.1348	-0.0728	0.2064	0.0905	0.0288	0.0411	0.18	-0.0142	0.064	0.1381	0.0003	0.14	44.309	72.399	20.976
8	-0.0101	0.2408	-0.0039	1.6165	-0.5908	-0.3001	0.0662	0.0149	0.0344	0.0944	-0.0031	0.153	-0.0652	0.0417	-0.0631	0.1279	-0.0429	0.057	0.1742	-0.0336	0.1041	48.783	86.098	23.037
9	1.2421	1.6672	1.2786	2.5747	1.1233	0.4138	-0.1128	0.1466	0.2154	-0.0495	-0.0716	0.3923	-0.0662	0.2042	0.1844	0.1383	-0.033	0.018	0.1581	-0.0447	0.1451	48.899	86.441	7.195
10	2.3968	-2.6164	0.1788	3.4691	-0.2383	-1.0176	0.1271	0.168	-0.0697	-0.2881	-0.1398	0.1598	0.073	0.0331	0.0127	0.1543	-0.0135	0.0166	0.1348	-0.0155	0.1475	40.844	69.339	2.78
11	1.7764	-1.5136	-1.9937	1.4454	0.9802	2.0353	-0.1243	0.0576	-0.2425	0.16	-0.0316	0.073	0.2643	-0.1569	0.1559	0.1321	-0.0076	-0.0151	0.0947	0.0229	0.2106	54.232	53.307	6.891
12	-0.7155	0.7265	0.1953	0.774	0.4309	0.7086	0.021	-0.0657	-0.1311	0.0217	-0.1104	-0.1184	-0.1518	0.0108	0.0894	0.1061	0.0401	0.0053	0.1351	0.0364	0.1836	61.845	57.066	7.711
13	3.0364	-3.5075	-2.0165	1.8252	0.7583	2.7411	0.1226	0.1503	-0.0642	-0.1161	-0.1	0.0128	-0.1548	0.0374	-0.0226	0.0788	-0.0175	0.0181	0.1684	-0.0537	0.1719	67.337	62.482	-3.109
14	1.6752	-0.5989	-1.0222	1.241	0.0971	0.5605	-0.0156	-0.0946	-0.0725	0.0124	0.0108	0.0093	-0.0775	0.0218	0.0049	0.1036	0.0029	-0.0114	0.1325	-0.0052	0.1545	58.696	62.899	3.016
15	9.7775	-6.7287	-7.6154	8.2446	13.4644	13.1927	0.9726	0.9779	0.8993	0.2036	-0.3248	-0.3859	0.4037	-0.7271	-0.6478	0.1493	0.0795	0.0213	0.0911	-0.0161	0.2102	64.903	50.823	-5.08
16	-0.1011	-0.4784	-0.7422	4.0757	1.6723	-2.1406	0.1373	-0.0819	0.0593	0.0721	-0.1693	-0.0799	0.0227	0.0156	0.032	0.1196	0.0173	-0.0075	0.191	-0.0024	0.0948	57.62	105.271	0.8
17	2.1833	1.1822	0.0096	16.7214	3.0834	0.0901	-0.1646	0.1483	0.0707	-0.5871	0.203	-0.1046	-0.0985	-0.0245	-0.0384	0.1925	-0.0642	0.0235	0.1029	0.0302	0.08	64.396	88.972	-5.293
18	2.1842	2.5736	1.1452	2.7582	1.1765	1.2089	-0.0541	0.0491	-0.1349	-0.0178	0.0844	-0.2277	0.0915	0.0297	-0.0303	0.1476	0.0258	0.0047	0.1015	0.0079	0.157	71.791	82.638	5.306
19	0.6031	-0.0603	-0.6813	0.9425	-0.0258	1.3727	-0.0162	-0.0439	0.007	0.1963	-0.0909	-0.033	0.0508	-0.0196	0.1071	0.1416	-0.0279	-0.0619	0.1835	-0.0212	0.0498	66.412	97.912	26.944
20	0.9544	0.4329	0.0224	10.607	-4.5237	7.9835	-0.009	0.118	0.4937	0.9217	0.2128	-0.0298	-1.2124	-0.2467	-0.2038	0.2533	-0.0937	-0.0745	0.1855	-0.131	0.0921	68.747	115.467	30.272
21	0.1476	-0.3629	0.6555	0.8695	-1.6502	1.8323	0.0157	0.0023	0.0784	0.0935	-0.0368	-0.0305	-0.0244	-0.0426	0.0211	0.1725	-0.0149	-0.0531	0.139	-0.069	0.1385	69.212	108.876	22.45
22	1.4344	-0.4639	-0.8349	0.34	-0.1103	0.864	0.0068	-0.1509	0.1529	0.0417	0.0452	-0.104	-0.1035	0.0379	-0.0521	0.1494	-0.0411	-0.0347	0.1223	-0.0482	0.162	73.646	102.831	19.555
23	0.531	0.6291	0.0885	1.5511	-0.0548	-0.1536	0.1402	-0.0237	0.0468	0.0847	-0.0466	-0.0268	0.0385	0.0357	-0.0936	0.1504	-0.0484	-0.0239	0.1982	-0.0049	0.0682	69.676	91.745	22.434
24	1.6611	2.4179	0.8407	2.6984	0.9719	3.7454	0.0209	-0.0333	0.0225	0.1777	-0.1636	-0.0042	0.3192	-0.0139	0.1427	0.1341	-0.0049	-0.0199	0.1241	0.0169	0.105	69.145	83.005	20.535
25	2.0395	0.874	-0.2209	1.0265	-0.5491	0.26	-0.1173	-0.1263	-0.0376	-0.2183	0.0183	-0.2258	0.1049	-0.0874	0.099	0.1469	0.0051	0.0235	0.1073	0.0233	0.1711	71.613	95.208	2.595
26	1.9206	-2.6459	0.2605	5.5659	0.0114	-0.1359	0.1197	-0.0877	0.3578	-0.2109	-0.1825	-0.3476	0.0461	-0.0967	0.0628	0.1054	0.0145	0.0224	0.1447	-0.0093	0.1605	68.93	116.374	3.455
27	6.7544	-4.7078	7.4082	3.2464	-4.4903	9.0273	-0.1285	-0.0885	0.2779	0.3232	0.1178	0.0068	-0.2745	0.0625	0.0107	0.1333	-0.0245	0.0484	0.0655	-0.0821	0.2016	60.854	124.212	9.964
28	1.3794	-0.9538	0.1439	1.0683	-0.7443	0.9905	0.0817	-0.0835	0.2988	-0.0947	0.0029	0.0019	0.2063	-0.087	-0.0845	0.0794	-0.0045	-0.0035	0.1176	-0.0541	0.2024	52.223	116.515	3.899
29	0.5363	-0.7654	0.3261	2.0365	-0.0108	0.0289	-0.05	-0.1371	0.1099	-0.0392	-0.0418	0.0322	0.063	-0.0412	0.0918	0.125	0.0212	-0.0184	0.1603	-0.0136	0.1322	57.664	113.275	3.562
30	7.35	-5.5093	-5.6374	15.0604	0.9226	2.0836	0.4238	0.1972	-0.0013	-0.4647	-0.5104	-0.2628	-0.1365	-0.2086	0.0865	0.0644	0.0418	-0.0724	0.0951	-0.0208	0.234	50.404	126.252	-3.835

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 20
2	X-RAY DIFFRACTION	2	A	21 - 39
3	X-RAY DIFFRACTION	3	A	40 - 48
4	X-RAY DIFFRACTION	4	A	49 - 100
5	X-RAY DIFFRACTION	5	A	101 - 140
6	X-RAY DIFFRACTION	6	A	141 - 164
7	X-RAY DIFFRACTION	7	A	165 - 195
8	X-RAY DIFFRACTION	8	A	196 - 236
9	X-RAY DIFFRACTION	9	A	237 - 256
10	X-RAY DIFFRACTION	10	A	257 - 268
11	X-RAY DIFFRACTION	11	A	269 - 293
12	X-RAY DIFFRACTION	12	A	294 - 310
13	X-RAY DIFFRACTION	13	A	311 - 323
14	X-RAY DIFFRACTION	14	A	324 - 352
15	X-RAY DIFFRACTION	15	A	353 - 360
16	X-RAY DIFFRACTION	16	B	3 - 13
17	X-RAY DIFFRACTION	17	B	14 - 30
18	X-RAY DIFFRACTION	18	B	31 - 60
19	X-RAY DIFFRACTION	19	B	61 - 115
20	X-RAY DIFFRACTION	20	B	116 - 142
21	X-RAY DIFFRACTION	21	B	143 - 164
22	X-RAY DIFFRACTION	22	B	165 - 196
23	X-RAY DIFFRACTION	23	B	197 - 223
24	X-RAY DIFFRACTION	24	B	224 - 241
25	X-RAY DIFFRACTION	25	B	242 - 264
26	X-RAY DIFFRACTION	26	B	265 - 279
27	X-RAY DIFFRACTION	27	B	280 - 294
28	X-RAY DIFFRACTION	28	B	295 - 322
29	X-RAY DIFFRACTION	29	B	323 - 354
30	X-RAY DIFFRACTION	30	B	355 - 361

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Open data

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Download

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Validation report

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Assembly

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About Yorodumi

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi