PDB-2wpw: Tandem GNAT protein from the clavulanic acid biosynthesis pathway...

ID or keywords:

Entry

Database: PDB / ID: 2wpw

Title

Tandem GNAT protein from the clavulanic acid biosynthesis pathway (without AcCoA)

Components

ORF14

Keywords

TRANSFERASE / ACETYL TRANSFERASE / ANTIBIOTIC BIOSYNTHESIS

Function / homology

Function and homology information

clavulanic acid biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function

Biological species

STREPTOMYCES CLAVULIGERUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.38 Å

Authors

Iqbal, A. / Arunlanantham, H. / McDonough, M.A. / Chowdhury, R. / Clifton, I.J.

Citation

Journal: Proteins / Year: 2010
Title: Crystallographic and mass spectrometric analyses of a tandem GNAT protein from the clavulanic acid biosynthesis pathway.
Authors: Iqbal, A. / Arunlanantham, H. / Brown, T. / Chowdhury, R. / Clifton, I.J. / Kershaw, N.J. / Hewitson, K.S. / McDonough, M.A. / Schofield, C.J.

History

Deposition	Aug 11, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 29, 2009	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2011	Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2	Mar 28, 2018	Group: Database references / Category: citation / citation_author Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name

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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PDBx/mmCIF format	2wpw.cif.gz	282.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2wpw.ent.gz	242 KB	Display	PDB format
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Validation report

Summary document	2wpw_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	2wpw_full_validation.pdf.gz	1.8 MB	Display
Data in XML	2wpw_validation.xml.gz	69.2 KB	Display
Data in CIF	2wpw_validation.cif.gz	96.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wp/2wpw ftp://data.pdbj.org/pub/pdb/validation_reports/wp/2wpw	HTTPS FTP

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Related structure data

Related structure data	2wpxC C: citing same article (ref.)
Similar structure data	6csj-5 6csj-7 2wpx-2 3tt2-d 5exv-1 3un5-1 5g0m-d 3qv2-d 1cc4-d 5g0q-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

2wpxC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (4) #97 - Jan 2008 Circadian Clock Proteins similarity (4)

Deposited unit

A: ORF14

B: ORF14

C: ORF14

D: ORF14

hetero molecules

150 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ORF14

hetero molecules

defined by software
37.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ORF14

hetero molecules

defined by software
37.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: ORF14

hetero molecules

defined by software
37.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: ORF14

hetero molecules

defined by software
37.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.449, 93.501, 126.430
Angle α, β, γ (deg.)	90.00, 97.86, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.999922, 0.010982, 0.006037), (0.010973, -0.999939, 0.00147), (0.006053, -0.001404, -0.999981)	-54.604, -7.039, -0.229
2	given	(0.999909, -0.013389, 0.00186), (0.013381, 0.9999, 0.004501), (-0.00192, -0.004476, 0.999988)	-8.748, 3.879, 62.541
3	given	(0.999961, 0.00439, -0.007683), (0.004437, -0.999971, 0.006173), (-0.007655, -0.006207, -0.999951)	-46.36, -10.507, 62.972

#1: Protein	ORF14 / TANDEM GCN5 RELATED N-ACETYL TRANSFERASE Mass: 36664.973 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: SELENO-METHIONINE LABELLED / Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q8KRB5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical	ChemComp-ACO / ACETYL COENZYME A Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula*: C₂₃H₃₈N₇O₁₇P₃S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1155 / 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: 3.05 Å³/Da / Density % sol: 59.7 % / Description: NONE
Crystal grow	pH: 6 Details: 3 MG/ML PROTEIN, 10% PEG8000, 0.1M CACODYLATE PH6, 0.2M SODIUM ACETATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97976
Detector	Type: ADSC CCD / Detector: CCD / Date: Sep 9, 2003 / Details: RH COATED MIRRORS
Radiation	Monochromator: SI (1 1 1) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97976 Å / Relative weight: 1
Reflection	Resolution: 2.38→32.4 Å / Num. obs: 68408 / % possible obs: 92.2 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / B_iso Wilson estimate: 44.8 Å² / R_merge(I) obs: 0.13 / Net I/σ(I): 6.5
Reflection shell	Resolution: 2.38→2.51 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 71.9

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0066	refinement
DENZO		data reduction
SCALEPACK		data scaling
SOLVE		phasing

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 2.38→32.4 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.915 / SU B: 18.005 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26563	3146	4.9 %	RANDOM
R_work	0.20868	-	-	-
obs	0.21151	61517	92.25 %	-

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: 29.885 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.97 Å²	0 Å²	-0.86 Å²
2-	-	-1.4 Å²	0 Å²
3-	-	-	0.19 Å²

Refinement step

Cycle: LAST / Resolution: 2.38→32.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9900	0	204	1155	11259

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.021	10364
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.134	1.972	14199
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.874	5	1296
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.289	22.174	460
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.41	15	1449
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.059	15	112
X-RAY DIFFRACTION	r_chiral_restr	0.202	0.2	1575
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	8092
X-RAY DIFFRACTION	r_gen_planes_other
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	0.86	1.5	6506
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.557	2	10386
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.954	3	3858
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.358	4.5	3813
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: 2.378→2.439 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.386	187	-
R_work	0.297	3515	-
obs	-	-	71.86 %

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	2.9705	-0.0211	-2.0444	1.4187	0.2058	5.7736	-0.0061	-0.3218	0.1869	-0.1201	-0.0108	0.3623	-0.3348	-0.29	0.0169	0.0612	0.0101	-0.0646	0.1271	-0.0062	0.1327	-40.9674	-1.3715	46.6469
2	1.3554	0.1564	-0.2897	1.5378	-0.0791	1.603	0.0273	-0.0023	0.0813	0.0165	-0.005	0.1256	-0.0454	-0.1389	-0.0222	0.0664	0.002	-0.0218	0.0553	-0.0025	0.0638	-32.1502	-5.4798	50.2659
3	2.0546	-0.037	-0.2293	3.0587	-0.8234	3.7241	0.02	-0.0021	0.2331	-0.0105	-0.0266	0.1211	-0.168	-0.0821	0.0066	0.079	0.001	-0.0171	0.0547	-0.0021	0.1042	-32.7707	6.4501	52.5608
4	0.1676	-0.1496	-0.252	1.3356	0.5581	2.8102	-0.001	-0.0896	0.1334	0.0047	0.053	-0.0871	-0.1196	0.1383	-0.052	0.0547	-0.0255	-0.0255	0.1291	-0.0404	0.1285	-18.111	3.0116	51.8727
5	1.8157	-0.076	0.1845	1.1172	-0.3346	1.1249	0.0597	0.138	-0.0535	-0.0685	-0.0087	-0.1386	0.0306	0.0918	-0.0511	0.0989	0.0057	-0.0356	0.0339	-0.027	0.0608	-8.0696	-25.8281	45.51
6	6.8917	0.1027	4.5596	0.1747	0.3539	3.74	-0.2587	-0.6209	0.5055	0.1457	0.1029	-0.1318	-0.1411	0.0048	0.1558	0.3469	-0.0544	-0.1541	0.3614	-0.0549	0.2083	-20.6198	-22.768	59.5705
7	3.1803	-1.9847	1.8972	1.9571	-1.1832	1.5003	0.014	-0.1016	0.0666	0.1291	0.0027	-0.0589	-0.0445	0.022	-0.0167	0.0975	-0.031	0.008	0.0764	0.0064	0.0669	-10.5308	-21.5845	44.7197
8	3.6048	-3.5646	-3.3315	3.9115	3.8024	4.5652	-0.3413	-0.4603	-0.0753	0.4144	0.3704	-0.1626	0.3492	0.5866	-0.0291	0.1104	-0.0605	-0.0127	0.2388	0.0781	0.2412	-11.7347	-1.8058	51.4833
9	0.4017	-0.1991	0.3158	0.8007	-0.1054	1.1385	0.0093	-0.0666	-0.1501	0.095	-0.0245	0.2714	0.1044	-0.2184	0.0152	0.1101	0.0106	0.0451	0.1147	-0.0118	0.1341	19.1727	-2.0366	-47.039
10	2.1625	-0.6429	0.471	3.9007	-0.6876	3.0262	0.0485	-0.0953	-0.1215	0.0594	-0.027	0.2364	0.1592	-0.0833	-0.0215	0.0547	-0.0125	0.005	0.0483	-0.0452	0.1065	22.5199	-10.2933	-53.4305
11	1.0928	-0.3925	1.447	3.0175	-0.8255	4.8904	-0.0538	0.108	-0.1144	0.1166	0.0312	-0.0786	0.014	0.1807	0.0226	0.0545	-0.0018	0.033	0.0634	-0.0295	0.0865	33.2632	-11.7285	-54.1306
12	0.6329	0.0088	-0.0881	1.2529	-0.0641	0.5734	0.016	0.0375	-0.0606	0.1486	0.0222	-0.1029	0.0201	0.04	-0.0382	0.0909	0.0136	-0.0025	0.1046	0.0064	0.0447	44.8849	10.1126	-46.7526
13	5.3929	-0.4019	-3.3156	0.8593	1.0036	6.6134	-0.101	0.6881	-0.3802	-0.4534	-0.0631	-0.1906	0.1021	0.0775	0.164	0.3416	0.0532	0.103	0.1552	-0.027	0.1477	34.3092	16.0607	-59.4535
14	3.3299	1.7481	-2.1227	1.6061	-1.2813	1.8957	-0.0508	0.077	-0.131	-0.0729	0.0251	-0.0607	0.111	0.0453	0.0257	0.1009	0.0279	-0.0183	0.0812	0.0113	0.0406	44.4485	15.7347	-45.3638
15	6.177	-1.0451	-1.5717	6.6769	2.781	2.1077	0.1761	0.4883	0.3867	-0.5864	0.1666	-0.6935	-0.4342	0.6786	-0.3427	0.1822	-0.1413	-0.0443	0.7373	-0.0321	0.2189	47.3891	1.1787	-46.4881
16	2.8108	2.2039	1.957	2.8183	1.884	2.2205	-0.1594	0.2868	0.0595	-0.0481	0.0732	0.0722	-0.0542	0.3533	0.0861	0.097	0.014	0.013	0.1221	0.0006	0.0709	40.3836	-6.3099	-51.4244
17	0.4522	0.2652	-0.4707	1.0788	0.2815	1.1283	0.0287	0.0557	0.0745	-0.0784	-0.0617	0.1717	-0.0819	-0.1804	0.033	0.1237	0.0039	-0.0318	0.1102	0.0067	0.1101	-26.2159	-8.0449	-13.7777
18	2.0094	0.0359	-0.1587	2.8357	-0.1937	3.4541	0.0437	-0.0088	0.1582	0.033	-0.0154	0.1357	-0.2086	-0.2399	-0.0283	0.1246	0.0079	-0.0294	0.0801	-0.0054	0.1092	-24.1208	2.6568	-9.4624
19	0.7129	-0.3525	-0.6762	1.167	0.8989	3.2167	-0.0102	-0.1048	0.1708	-0.0502	0.0095	-0.1392	-0.1541	0.152	0.0007	0.0818	-0.0225	-0.0109	0.1103	-0.0107	0.0769	-8.7592	-0.6675	-11.1277
20	2.3344	-0.2301	0.3435	1.226	0.1658	1.1993	0.144	0.0573	0.0275	-0.0416	-0.0283	-0.1083	-0.0397	0.1483	-0.1157	0.1105	0.0123	-0.0344	0.0459	-0.0168	0.0841	0.263	-29.5325	-16.5337
21	3.7219	-0.3355	3.0898	0.3081	0.6234	5.8889	-0.171	-0.5152	0.3148	0.1794	0.1571	-0.1198	0.0962	0.2552	0.0138	0.345	-0.1189	-0.1007	0.3546	-0.0061	0.119	-12.8198	-26.4256	-3.312
22	1.993	-1.2977	0.8382	1.6463	-0.6302	0.392	0.0234	-0.1395	0.0884	0.147	-0.0033	-0.0718	-0.0381	-0.0399	-0.0201	0.1272	-0.0249	0.0305	0.1052	-0.0094	0.1188	-1.9301	-24.2371	-17.4633
23	3.9738	2.4225	-1.8828	12.6023	7.8224	8.1379	-0.0679	-0.143	0.1933	0.941	0.4643	-0.1673	0.7793	0.5261	-0.3964	0.3579	-0.1299	-0.1432	0.4944	-0.0001	0.5208	6.9354	-11.1508	-11.549
24	2.4778	-2.379	-2.2297	3.5305	2.5722	3.5259	-0.1401	-0.1482	0.023	0.0708	0.0736	-0.1118	0.1257	0.2418	0.0665	0.0735	-0.0401	-0.0366	0.1135	0.0226	0.0788	-5.8997	-4.1116	-11.1546
25	0.3314	-0.18	0.583	0.3635	-0.1846	1.0948	0.0704	-0.0732	-0.0912	0.0219	-0.0223	0.2531	0.1584	-0.1429	-0.0481	0.1521	0.0087	0.0547	0.1395	-0.0047	0.2266	10.8968	-5.3531	15.9809
26	1.7183	-0.0073	0.3023	2.2562	0.0572	2.2164	0.0293	0.0205	-0.1256	0.0653	0.022	0.1269	0.0619	-0.0021	-0.0513	0.075	-0.0045	-0.002	0.0247	-0.0326	0.0842	19.3185	-14.7995	8.72
27	0.5491	-0.0834	-0.1825	0.9898	-0.2697	0.1716	0.0272	-0.0631	0.0214	0.1121	-0.0559	-0.102	-0.0409	0.0827	0.0287	0.1206	0.0056	-0.0101	0.0976	0.0084	0.0439	37.8675	10.8914	18.1164
28	4.4933	2.3085	-0.6898	3.478	1.3439	1.3655	-0.0447	0.7989	-0.113	0.0009	0.1773	-0.2618	0.0441	-0.2878	-0.1325	0.3198	0.1086	-0.0177	0.2485	-0.0144	0.0525	31.3568	14.4662	-3.1367
29	1.6371	0.5884	-0.3387	0.7431	-0.1948	0.4775	-0.0349	0.1393	-0.1733	-0.149	-0.018	-0.0179	0.1201	0.063	0.0529	0.1171	0.0196	0.002	0.088	-0.0004	0.0583	33.6322	11.8306	14.2713
30	1.8425	0.2513	-0.2896	5.6489	3.2517	4.8573	-0.034	-0.0144	0.0535	-0.0512	0.0336	0.1187	-0.2299	0.191	0.0003	0.1099	0.0093	-0.0125	0.1287	0.0154	0.078	33.1026	3.6412	22.9785
31	5.0908	1.2615	-1.7493	7.8976	3.1655	5.8662	0.0836	1.0261	-0.2582	-0.6834	0.1108	-0.7467	-0.0232	0.1547	-0.1944	0.1521	0.0835	0.0185	0.322	-0.0133	0.1291	43.7879	-1.6505	17.6272
32	3.8079	2.3546	2.8975	2.6483	1.9183	3.6613	-0.1936	0.4356	0.1148	-0.1396	0.0373	0.256	-0.0561	0.3175	0.1563	0.1024	0.0347	0.0076	0.127	-0.0221	0.0937	26.7199	-14.3732	6.7558

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 30
2	X-RAY DIFFRACTION	2	A	31 - 85
3	X-RAY DIFFRACTION	3	A	86 - 114
4	X-RAY DIFFRACTION	4	A	115 - 163
5	X-RAY DIFFRACTION	5	A	164 - 198
6	X-RAY DIFFRACTION	6	A	199 - 232
7	X-RAY DIFFRACTION	7	A	233 - 304
8	X-RAY DIFFRACTION	8	A	305 - 339
9	X-RAY DIFFRACTION	9	B	6 - 68
10	X-RAY DIFFRACTION	10	B	69 - 112
11	X-RAY DIFFRACTION	11	B	113 - 145
12	X-RAY DIFFRACTION	12	B	146 - 197
13	X-RAY DIFFRACTION	13	B	198 - 232
14	X-RAY DIFFRACTION	14	B	233 - 299
15	X-RAY DIFFRACTION	15	B	300 - 314
16	X-RAY DIFFRACTION	16	B	315 - 339
17	X-RAY DIFFRACTION	17	C	7 - 85
18	X-RAY DIFFRACTION	18	C	86 - 115
19	X-RAY DIFFRACTION	19	C	116 - 163
20	X-RAY DIFFRACTION	20	C	164 - 199
21	X-RAY DIFFRACTION	21	C	200 - 232
22	X-RAY DIFFRACTION	22	C	233 - 309
23	X-RAY DIFFRACTION	23	C	310 - 314
24	X-RAY DIFFRACTION	24	C	315 - 339
25	X-RAY DIFFRACTION	25	D	7 - 68
26	X-RAY DIFFRACTION	26	D	69 - 153
27	X-RAY DIFFRACTION	27	D	154 - 197
28	X-RAY DIFFRACTION	28	D	198 - 217
29	X-RAY DIFFRACTION	29	D	218 - 293
30	X-RAY DIFFRACTION	30	D	294 - 309
31	X-RAY DIFFRACTION	31	D	310 - 323
32	X-RAY DIFFRACTION	32	D	324 - 339

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