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

ID or keywords:

Entry

Database: PDB / ID: 2wpx

Title

Tandem GNAT protein from the clavulanic acid biosynthesis pathway (with 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 /

MOLECULAR REPLACEMENT / Resolution: 2.31 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 / Version format compliance
Revision 1.2	Jun 11, 2014	Group: Data collection / Other
Revision 1.3	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
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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	2wpx.cif.gz	152.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2wpx.ent.gz	121.3 KB	Display	PDB format
PDBx/mmJSON format	2wpx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2wpx_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	2wpx_full_validation.pdf.gz	1.2 MB	Display
Data in XML	2wpx_validation.xml.gz	35.9 KB	Display
Data in CIF	2wpx_validation.cif.gz	51.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wp/2wpx ftp://data.pdbj.org/pub/pdb/validation_reports/wp/2wpx	HTTPS FTP

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Related structure data

Related structure data	2wpwSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1att-1 7c49-2 4fzr-d 6aio-2 3k7q-d 4imh-2 2dh3-1 3ubt-1 1jdj-d 3nn6-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) 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	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (4) #97 - Jan 2008 Circadian Clock Proteins similarity (4)

Deposited unit

A: ORF14

B: ORF14

hetero molecules

74.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ORF14

hetero molecules

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

2

B: ORF14

hetero molecules

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

Unit cell

Length a, b, c (Å)	151.985, 70.093, 106.287
Angle α, β, γ (deg.)	90.00, 134.38, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (-0.021425, -9.9E-5, -0.99977), (-0.000298, -1, 0.000106), (-0.99977, 0.0003, 0.021425)
Vector: 0.019, 159.876, -0.007)

#1: Protein	ORF14 / TANDEM GCN5 RELATED N-ACETYL TRANSFERASE Mass: 36336.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source 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.: 2 / Source method: obtained synthetically / Formula*: C₂₃H₃₈N₇O₁₇P₃S
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.79 Å³/Da / Density % sol: 55.97 % / Description: NONE
Crystal grow	pH: 6.5 Details: 3MG/ML PROTEIN, THREE-FOLD MOLAR EXCESS ACCOA, 1M SODIUM CITRATE, 0.07M CACODYLATE PH6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
Detector	Type: ADSC CCD / Detector: CCD / Date: May 31, 2003
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.488 Å / Relative weight: 1
Reflection	Resolution: 2.31→32.2 Å / Num. obs: 34742 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / B_iso Wilson estimate: 35.9 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 11.6
Reflection shell	Resolution: 2.31→2.45 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.24 / Mean I/σ(I) obs: 5.7 / % possible all: 95.3

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WPW

2wpw

Resolution: 2.31→31.82 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.874 / SU B: 14.298 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.253	1662	4.9 %	RANDOM
R_work	0.18785	-	-	-
obs	0.19104	32050	96.31 %	-

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: 22.425 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.06 Å²	0 Å²	-0.71 Å²
2-	-	0.22 Å²	0 Å²
3-	-	-	-0.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.31→31.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4942	0	114	590	5646

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.021	5184
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.286	1.973	7098
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.37	5	648
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.643	22.105	228
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.981	15	722
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.214	15	56
X-RAY DIFFRACTION	r_chiral_restr	0.214	0.2	786
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	4038
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	0.794	1.5	3252
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.372	2	5188
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.586	3	1932
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.893	4.5	1910
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: 2.314→2.374 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.309	101	-
R_work	0.225	2062	-
obs	-	-	85.39 %

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	4.1542	0.5472	-0.2733	3.7546	-0.4608	2.2144	-0.0082	0.375	-0.2989	-0.1352	0.0096	0.0444	0.1788	-0.0552	-0.0013	0.0758	-0.0032	-0.0073	0.0774	-0.0264	0.0238	-77.8777	85.6377	41.4783
2	1.1967	-0.3233	0.1344	0.8428	0.2423	0.3692	0.011	-0.0252	-0.006	0.0201	0.034	0.0749	0.0314	-0.0179	-0.045	0.02	-0.0015	-0.0168	0.0045	0.0097	0.0369	-77.3744	86.2326	51.2853
3	2.2117	0.586	-2.2556	1.1256	-1.5087	8.023	-0.0282	0.0242	0.0446	0.0149	0.0678	0.1825	-0.1119	-0.2264	-0.0397	0.0311	0.0187	-0.0268	0.0156	-0.0071	0.0616	-87.4967	92.2766	49.2823
4	4.761	-0.4822	1.2938	0.5158	0.0123	0.4953	-0.0517	0.0548	0.3488	-0.0004	-0.0337	0.0547	-0.1155	0.001	0.0854	0.1178	-0.0019	0.0158	0.0083	0.0085	0.0673	-77.8164	106.5983	52.4309
5	1.3936	0.8723	-0.3335	2.2123	-0.7354	0.7753	0.0617	0.0013	0.0644	0.0751	-0.0274	-0.0393	-0.0329	0.1112	-0.0343	0.0294	0.006	-0.0091	0.0532	-0.0091	0.0479	-53.4189	97.8145	68.4386
6	2.0352	-1.39	-1.9882	1.3276	1.6481	2.2264	0.0846	-0.1007	0.1715	-0.0409	-0.1612	0.2279	-0.2255	-0.133	0.0766	0.3995	0.0918	-0.0163	0.2745	-0.1124	0.4298	-70.4525	89.781	74.7907
7	0.7911	0.8625	0.2246	2.9646	2.1358	1.8312	0.0282	-0.0114	-0.0114	0.0537	0.1559	-0.192	0.0246	0.1634	-0.1841	0.0076	0.0012	-0.0091	0.0159	-0.0165	0.0268	-57.7885	92.8603	69.4655
8	4.0043	2.0387	4.1108	3.0359	0.0491	6.3111	0.2037	-0.2699	0.0369	0.238	-0.1516	0.1023	0.0794	-0.2677	-0.0521	0.0264	-0.016	-0.007	0.0185	-0.0001	0.0344	-60.3083	94.7545	56.7426
9	2.4635	-1.8995	-2.7074	2.9193	2.6457	9.4718	0.0741	0.0771	0.0349	0.1228	-0.0825	0.1097	-0.4218	-0.3497	0.0084	0.0677	0.0039	-0.0051	0.0222	0.0164	0.0463	-56.6247	103.0468	70.4901
10	8.7541	-7.5763	6.721	8.7494	-3.6469	7.6907	0.1222	0.5861	0.4466	-0.27	-0.1757	-0.8369	0.1124	0.9435	0.0535	0.1194	0.0391	0.1037	0.176	0.0366	0.1849	-51.5965	95.7908	53.1416
11	5.2626	0.4463	2.1592	5.4972	2.2626	1.6823	-0.0481	-0.1475	0.1372	0.1517	0.0066	0.0101	0.034	-0.0553	0.0415	0.0397	0.0018	0.0025	0.0141	0.0084	0.0193	-66.6286	108.5247	59.6425
12	0.51	1.6435	-1.1348	9.1881	-1.1044	4.569	-0.0075	-0.0337	-0.0385	0.1528	-0.1511	0.2099	0.074	-0.1838	0.1586	0.0506	0.0466	0.0303	0.1501	0.0873	0.0924	-90.3989	99.178	56.9673
13	2.3466	0.6349	0.5144	3.2744	1.3867	3.8886	-0.0351	0.0005	0.1108	0.1303	0.1134	-0.2394	-0.0989	0.3987	-0.0783	0.0149	-0.0132	-0.0197	0.0553	0.0076	0.0571	-40.4656	72.5142	77.3234
14	2.2795	-0.0279	1.3672	0.3924	-0.396	2.4309	-0.0885	-0.0343	0.1245	0.1195	0.0484	-0.0336	-0.1117	-0.0101	0.0401	0.042	0.0181	-0.0184	0.0086	-0.0088	0.0187	-48.4454	76.2497	77.5555
15	8.3565	-1.1542	-1.666	0.9474	0.0466	2.0749	-0.0904	-0.062	-0.1817	0.1806	0.0104	0.0488	0.0598	-0.041	0.0799	0.0503	-0.0051	0.0006	0.0035	0.0031	0.014	-48.5035	68.8078	87.7483
16	0.9709	-0.1241	1.8907	0.2616	-0.0936	5.1647	0.058	0.069	-0.1246	-0.0219	-0.0129	-0.0226	0.3444	0.1574	-0.0452	0.0655	0.0029	0.0091	0.007	0.0021	0.0842	-53.0047	53.3905	71.4147
17	0.7595	2.0609	0.8639	7.8569	3.1807	1.3075	-0.0148	0.0847	-0.0077	-0.2696	-0.1388	0.3754	-0.0743	-0.0684	0.1536	0.0718	-0.0099	-0.0208	0.1209	-0.0642	0.0841	-72.8555	68.2797	57.4608
18	5.0753	1.1373	-4.5018	0.2829	-1.0521	4.2826	-0.044	-0.0926	-0.1986	0.0213	0.0197	0.0429	0.2307	-0.1929	0.0243	0.3932	-0.0972	0.0158	0.3308	0.0965	0.3247	-74.4299	69.8584	72.6041
19	2.2984	-1.4778	0.6942	6.1068	1.2378	0.7598	-0.0392	-0.0762	-0.1392	0.0771	-0.0486	0.4097	-0.0071	-0.0645	0.0878	0.0266	-0.0065	0.0033	0.055	-0.0324	0.049	-57.5207	72.3483	62.2535
20	8.6713	1.1707	1.0409	0.2313	0.1004	0.2982	-0.0408	-0.1904	0.0565	0.0195	-0.0069	0.0294	-0.002	-0.0517	0.0477	0.0162	0.0066	0.0081	0.0114	-0.0037	0.029	-63.9081	63.992	59.7363
21	9.5411	3.3195	-3.1849	2.788	-1.2526	3.4269	-0.0184	-0.1749	-0.1732	0.1295	0.0974	0.1243	0.0633	-0.0081	-0.079	0.0366	0.0237	-0.008	0.0256	0.0135	0.0477	-69.3458	56.8806	57.9995
22	2.5778	0.1613	3.3053	4.7224	-4.0641	8.6595	-0.0447	0.3865	0.0352	-0.4106	0.0841	0.0087	0.1803	0.3171	-0.0394	0.068	0.0202	0.014	0.1	0.0023	0.0445	-52.2303	63.6339	53.9023
23	2.959	1.8278	2.4048	4.1012	0.141	5.3281	0.1267	-0.0494	-0.0991	0.1366	-0.0393	0.2668	0.2158	-0.2223	-0.0875	0.0198	-0.0103	0.0057	0.0136	-0.0095	0.0488	-58.515	51.0176	68.0158
24	4.1492	-1.4011	-0.7481	9.6003	-0.5119	0.1995	0.0508	-0.4083	0.0645	0.3843	-0.0282	-0.0683	-0.0444	0.0813	-0.0226	0.0187	-0.0125	-0.0009	0.0976	0.0665	0.0962	-55.1883	60.7117	91.4174

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 36
2	X-RAY DIFFRACTION	2	A	37 - 83
3	X-RAY DIFFRACTION	3	A	84 - 122
4	X-RAY DIFFRACTION	4	A	123 - 162
5	X-RAY DIFFRACTION	5	A	163 - 198
6	X-RAY DIFFRACTION	6	A	199 - 228
7	X-RAY DIFFRACTION	7	A	229 - 250
8	X-RAY DIFFRACTION	8	A	251 - 268
9	X-RAY DIFFRACTION	9	A	269 - 293
10	X-RAY DIFFRACTION	10	A	294 - 302
11	X-RAY DIFFRACTION	11	A	303 - 328
12	X-RAY DIFFRACTION	12	A	329 - 338
13	X-RAY DIFFRACTION	13	B	5 - 40
14	X-RAY DIFFRACTION	14	B	41 - 69
15	X-RAY DIFFRACTION	15	B	70 - 120
16	X-RAY DIFFRACTION	16	B	121 - 177
17	X-RAY DIFFRACTION	17	B	178 - 197
18	X-RAY DIFFRACTION	18	B	198 - 227
19	X-RAY DIFFRACTION	19	B	228 - 237
20	X-RAY DIFFRACTION	20	B	238 - 268
21	X-RAY DIFFRACTION	21	B	269 - 293
22	X-RAY DIFFRACTION	22	B	294 - 303
23	X-RAY DIFFRACTION	23	B	304 - 328
24	X-RAY DIFFRACTION	24	B	329 - 338

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