PDB-6xg1: Class C beta-lactamase from Escherichia coli

ID or keywords:

Entry

Database: PDB / ID: 6xg1

Title

Class C beta-lactamase from Escherichia coli

Components

Beta-lactamase

Keywords

HYDROLASE / class C beta-lactamase / structural genomic / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase / beta-lactamase activity / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.22 Å

Authors

Chang, C. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Class C beta-lactamase from Escherichia coli
Authors: Chang, C. / Maltseva, N. / Endres, M. / Joachimiak, A.

History

Deposition	Jun 16, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 24, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6xg1.cif.gz	314.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6xg1.ent.gz	254.6 KB	Display	PDB format
PDBx/mmJSON format	6xg1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6xg1_validation.pdf.gz	446.5 KB	Display	wwPDB validaton report
Full document	6xg1_full_validation.pdf.gz	450.1 KB	Display
Data in XML	6xg1_validation.xml.gz	34.1 KB	Display
Data in CIF	6xg1_validation.cif.gz	52.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xg/6xg1 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/6xg1	HTTPS FTP

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Related structure data

Related structure data	6wa7 PDB Unreleased entryS 6whf 6xfs S: Starting model for refinement
Similar structure data	2ffy-1 6xfs-1 1ll5-2 1llb-1 2zc7-1 6whf-2 1l0g-2 2r9w-2 3gv9-1 2pu4-2 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
Other databases	TargetTrack: CSGID-IDP97257

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#29 - May 2002 Penicillin-binding Proteins similarity (3) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

A: Beta-lactamase

hetero molecules

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

2

B: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	154.865, 46.176, 108.909
Angle α, β, γ (deg.)	90.000, 116.540, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-813- HOH
2	1	B-833- HOH

#1: Protein	Beta-lactamase Mass: 39859.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla(ampc-EC31), blaEC / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q104Z6, UniProt: P00811*PLUS, beta-lactamase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 714 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.71 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M HEPES, 10% 2-propanol, 20% PEG4000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97911 Å

Detector

Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 21, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97911 Å / Relative weight: 1

Reflection

Resolution: 1.22→50 Å / Num. obs: 202144 / % possible obs: 98.3 % / Redundancy: 5.4 % / R_merge(I) obs: 0.083 / R_pim(I) all: 0.039 / R_rim(I) all: 0.092 / Χ²: 0.85 / Net I/σ(I): 5.7 / Num. measured all: 1082465

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.22-1.24	5.1	0.587	9850	0.806	0.283	0.654	0.494	96.5
1.24-1.26	5.4	0.527	9952	0.844	0.248	0.584	0.505	97.6
1.26-1.29	5.3	0.438	10075	0.886	0.207	0.486	0.538	97.8
1.29-1.31	5.3	0.4	9948	0.897	0.19	0.444	0.558	98
1.31-1.34	5.2	0.36	9978	0.913	0.173	0.4	0.578	97.7
1.34-1.37	5.1	0.314	9977	0.919	0.153	0.351	0.6	97.2
1.37-1.41	5.5	0.277	10085	0.942	0.129	0.306	0.617	98.5
1.41-1.45	5.5	0.239	10136	0.954	0.111	0.264	0.664	98.6
1.45-1.49	5.4	0.205	10099	0.962	0.097	0.228	0.721	98.7
1.49-1.54	5.3	0.181	10048	0.967	0.086	0.201	0.788	98.2
1.54-1.59	5	0.162	9961	0.967	0.08	0.181	0.876	97.3
1.59-1.66	5.5	0.148	10230	0.976	0.068	0.163	0.954	99.3
1.66-1.73	5.5	0.137	10173	0.977	0.064	0.151	1.037	99.2
1.73-1.82	5.5	0.127	10167	0.978	0.059	0.14	1.158	99
1.82-1.94	5.4	0.118	10185	0.978	0.056	0.131	1.185	98.7
1.94-2.09	5.3	0.108	10084	0.983	0.051	0.12	1.115	98
2.09-2.3	5.6	0.1	10257	0.985	0.046	0.11	1.099	99.5
2.3-2.63	5.5	0.094	10238	0.985	0.044	0.105	1.237	99
2.63-3.31	5.4	0.083	10216	0.99	0.039	0.092	1.089	98.1
3.31-50	5.4	0.067	10485	0.992	0.032	0.074	1.035	98.7

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
SBC-Collect		data collection
SCALEPACK		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6WA7

6wa7
PDB Unreleased entry

Resolution: 1.22→43.81 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1781	10085	4.99 %
R_work	0.1609	192052	-
obs	0.1618	202137	97.81 %

Solvent computation

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

Displacement parameters

B_iso max: 108.58 Å² / B_iso mean: 24.2458 Å² / B_iso min: 11.42 Å²

Refinement step

Cycle: final / Resolution: 1.22→43.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5624	0	28	714	6366
B_iso mean	-	-	55	33.33	-
Num. residues	-	-	-	-	720

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.22-1.23	0.2435	280	0.2447	5348	5628	82
1.23-1.24	0.2647	316	0.2403	6365	6681	97
1.24-1.26	0.2391	315	0.2189	6330	6645	98
1.26-1.28	0.2416	326	0.2121	6368	6694	98
1.28-1.29	0.2131	339	0.2018	6324	6663	98
1.29-1.31	0.2062	309	0.2018	6440	6749	98
1.31-1.33	0.2126	347	0.198	6362	6709	98
1.33-1.35	0.2091	383	0.196	6327	6710	98
1.35-1.37	0.221	342	0.1952	6310	6652	97
1.37-1.39	0.215	330	0.1861	6421	6751	99
1.39-1.42	0.1862	321	0.18	6409	6730	98
1.42-1.44	0.2055	343	0.1757	6493	6836	99
1.44-1.47	0.2001	347	0.1705	6372	6719	99
1.47-1.5	0.1778	355	0.1646	6357	6712	99
1.5-1.53	0.1962	350	0.1638	6432	6782	98
1.53-1.57	0.1786	329	0.1544	6361	6690	98
1.57-1.61	0.1667	330	0.152	6368	6698	97
1.61-1.65	0.1734	335	0.1504	6569	6904	99
1.65-1.7	0.1721	337	0.1521	6456	6793	99
1.7-1.75	0.1837	357	0.1531	6481	6838	99
1.75-1.82	0.1616	331	0.16	6474	6805	99
1.82-1.89	0.1811	333	0.1603	6493	6826	99
1.89-1.98	0.201	324	0.1627	6355	6679	97
1.98-2.08	0.1779	346	0.16	6507	6853	99
2.08-2.21	0.1828	316	0.1587	6564	6880	100
2.21-2.38	0.1809	334	0.1622	6531	6865	99
2.38-2.62	0.1676	353	0.165	6510	6863	99
2.62-3	0.1819	347	0.1724	6420	6767	97
3-3.78	0.1758	324	0.1572	6629	6953	99
3.78-43.81	0.158	386	0.1406	6676	7062	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	0.2121	0.112	-0.0797	0.2845	-0.0687	0.0352	0.0226	0.396	0.1447	-0.4259	-0.0405	0.0795	-0.361	-0.1599	-0.0162	0.3152	0.062	-0.0577	0.2676	0.0418	0.2279	24.6737	14.3431	13.682
2	0.2198	0.1472	0.0655	0.423	-0.0817	0.32	-0.0046	0.0452	-0.0449	-0.0485	-0.0298	0.1129	-0.0339	-0.155	0.0009	0.1493	0.0164	-0.0204	0.1872	-0.0327	0.1554	21.2498	0.7043	21.5006
3	0.0236	0.0664	0.0142	0.1445	0.1103	0.1195	-0.0155	-0.1757	-0.1373	0.2749	-0.0438	0.0841	0.1823	-0.1225	-0.0029	0.2559	-0.0265	0.0059	0.2129	0.0423	0.1935	29.0241	-12.3632	51.3289
4	0.248	0.0673	-0.0613	0.3584	-0.0075	0.0062	0.0179	-0.0489	-0.0553	0.1078	-0.0205	-0.0954	0.1012	0.0072	0	0.1937	-0.0128	-0.026	0.1378	0.0085	0.1729	38.6534	-11.1521	42.1861
5	0.1356	-0.032	-0.0985	0.0903	-0.0874	0.1264	-0.0217	0.0592	-0.1487	-0.0557	-0.0523	0.107	0.2118	-0.1959	-0.0058	0.1698	-0.0433	0.0074	0.1993	-0.0269	0.2136	16.5999	-10.7911	34.2648
6	0.1731	0.1517	-0.1083	0.2547	-0.1926	0.407	-0.0067	0.0562	-0.0317	-0.0602	0.0008	0.01	0.1262	-0.0811	0	0.1719	-0.0048	-0.0212	0.2031	-0.0338	0.1746	24.2716	-6.3847	23.1731
7	0.4779	0.0551	0.2132	0.455	-0.0371	0.558	-0.0194	-0.0077	0.0422	0.0106	-0.0349	0.0097	-0.0881	-0.0294	0	0.1369	0.0049	-0.0003	0.1398	-0.0142	0.1582	28.3565	8.611	34.1405
8	0.0271	-0.0023	0.0612	0.1366	-0.0044	0.158	0.0842	0.3107	-0.0312	-0.5397	-0.1149	-0.1583	0.4334	0.121	-0.0065	0.453	0.0022	0.0295	0.2076	-0.0062	0.2467	68.0146	-9.4875	3.879
9	0.076	-0.0155	-0.1069	0.0934	0.0741	0.1135	-0.0252	-0.0103	-0.2387	-0.2293	0.0535	-0.1612	0.1809	0.1341	0.0008	0.2913	0.0193	0.0158	0.2013	0.0107	0.197	71.5131	-2.2329	6.5094
10	1.1509	0.0965	-0.5258	0.6532	-0.2464	0.2324	0.1059	-0.1591	0.24	-0.0345	-0.0387	-0.0209	-0.0969	0.0911	0.0758	0.1694	-0.0352	0.0236	0.1807	-0.0267	0.1949	66.0187	14.5293	20.8818
11	0.3184	0.0997	-0.1795	0.2998	0.0375	0.2711	0.0707	-0.0357	0.1332	0.0255	0.042	0.1592	-0.2199	0.0995	0.0018	0.1999	-0.0258	0.0355	0.1687	-0.0076	0.221	53.6521	16.4037	32.096
12	0.116	-0.0707	0.1199	0.1184	0.0724	0.1052	0.1003	-0.0566	0.248	-0.2581	0.1246	-0.1304	-0.3899	0.2933	0.0169	0.2404	-0.0691	0.0669	0.2204	-0.0365	0.2728	73.0674	19.4529	18.9293
13	0.2065	-0.0841	-0.1369	0.1715	0.0054	0.1914	0.1016	-0.0081	0.1578	-0.1669	-0.0006	-0.0348	-0.1588	-0.0441	0.0128	0.2599	-0.0009	0.0199	0.1957	0.0386	0.1938	59.9724	14.9316	8.3928
14	0.0792	-0.0168	-0.0063	1.129	-0.1541	0.0753	0.0598	-0.1872	0.0092	-0.0691	0.0594	-0.3526	-0.0456	0.409	0.0493	0.1427	-0.0309	0.0056	0.3332	-0.0377	0.242	78.7379	6.7752	22.8173
15	0.0697	-0.0605	-0.0509	0.0002	0.0999	0.0539	-0.0917	-0.1783	-0.1603	-0.0144	0.0487	-0.0232	0.1835	0.0367	0.0001	0.2092	-0.0138	0.0018	0.1985	0.0246	0.2019	63.2005	-4.4033	28.1691
16	0.0217	-0.0409	0.0756	0.2084	-0.0826	0.1054	0.088	0.0635	-0.1926	0.0048	-0.002	-0.0227	0.1859	0.1521	-0	0.1857	0.0169	-0.0169	0.2336	0.005	0.1992	60.8885	-1.4124	32.6404
17	0.3517	0.1607	-0.3809	0.1254	0.0776	0.3615	-0.0768	-0.0594	-0.1078	-0.1505	0.0569	-0.0333	0.1254	0.0352	-0	0.2017	-0.0084	-0.0006	0.1636	0.025	0.1749	65.6393	-3.4489	15.4565

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 30 through 50 )	A	30 - 50
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 51 through 106 )	A	51 - 106
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 107 through 125 )	A	107 - 125
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 126 through 189 )	A	126 - 189
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 190 through 219 )	A	190 - 219
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 220 through 265 )	A	220 - 265
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 266 through 388 )	A	266 - 388
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 29 through 50 )	B	29 - 50
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 51 through 71 )	B	51 - 71
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 72 through 125 )	B	72 - 125
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 126 through 189 )	B	126 - 189
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 190 through 219 )	B	190 - 219
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 220 through 253 )	B	220 - 253
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 254 through 282 )	B	254 - 282
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 283 through 314 )	B	283 - 314
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 315 through 337 )	B	315 - 337
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 338 through 388 )	B	338 - 388

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