PDB-5haq: OXa-48 beta-lactamase mutant - S70G

ID or keywords:

Entry

Database: PDB / ID: 5haq

Title

OXa-48 beta-lactamase mutant - S70G

Components

Beta-lactamase

Keywords

HYDROLASE / serine beta-lactamase

Function / homology

Function and homology information

penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.14 Å

Authors

Stojanoski, V. / Adamski, C.J. / Hu, L. / Mehta, S.C. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.G.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI32956	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI55449	United States

Citation

Journal: Biochemistry / Year: 2016
Title: Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine beta-Lactamases by Relieving Steric Strain.
Authors: Stojanoski, V. / Adamski, C.J. / Hu, L. / Mehta, S.C. / Sankaran, B. / Zwart, P. / Prasad, B.V. / Palzkill, T.

History

Deposition	Dec 30, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 7, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 29, 2017	Group: Structure summary
Revision 1.2	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5haq.cif.gz	211.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5haq.ent.gz	176.4 KB	Display	PDB format
PDBx/mmJSON format	5haq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5haq_validation.pdf.gz	443.5 KB	Display	wwPDB validaton report
Full document	5haq_full_validation.pdf.gz	444.7 KB	Display
Data in XML	5haq_validation.xml.gz	20.8 KB	Display
Data in CIF	5haq_validation.cif.gz	29.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ha/5haq ftp://data.pdbj.org/pub/pdb/validation_reports/ha/5haq	HTTPS FTP

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Related structure data

Related structure data	5haiC 5hapC 5harC C: citing same article (ref.)
Similar structure data	6p96-d 5dts-2 4s2j-1 5dts-4 4s2k-1 4wmc-1 1389 6q5b-1 4s2k-2 5fat-d 5dtk-1 6v1o-2 6v1o-1 5fas-d 6goa-1 4s2p-d 5oe0-d 5hfo-d 6goa-2 5dtk-2 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

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	72.660, 73.611, 106.360
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Beta-lactamase Mass: 27938.631 Da / Num. of mol.: 2 / Fragment: UNP residues 25-265 / Mutation: S70G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical	ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.55 Å³/Da / Density % sol: 51.67 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2M sodium formate, 0.1M cadmium chloride, and 25% w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.997 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2015
Radiation	Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.997 Å / Relative weight: 1
Reflection	Resolution: 2.14→60 Å / Num. obs: 32095 / % possible obs: 99.8 % / Redundancy: 6.5 % / R_merge(I) obs: 0.05 / Net I/σ(I): 9.2
Reflection shell	Resolution: 2.14→2.22 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.32 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Resolution: 2.14→60 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 23.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2113	1623	5.09 %	Random selection
R_work	0.184	-	-	-
obs	0.1854	32095	99.7 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.14→60 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3944	0	10	191	4145

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4064
X-RAY DIFFRACTION	f_angle_d	0.893	5481
X-RAY DIFFRACTION	f_dihedral_angle_d	20.391	2371
X-RAY DIFFRACTION	f_chiral_restr	0.091	575
X-RAY DIFFRACTION	f_plane_restr	0.003	704

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 (%)
2.14-2.1734	0.3334	113	0.2777	2631	X-RAY DIFFRACTION	100
2.1734-2.2091	0.266	150	0.2675	2606	X-RAY DIFFRACTION	99
2.2091-2.2472	0.2895	163	0.2541	2591	X-RAY DIFFRACTION	100
2.2472-2.288	0.3117	140	0.2491	2587	X-RAY DIFFRACTION	100
2.288-2.332	0.3212	122	0.2437	2614	X-RAY DIFFRACTION	99
2.332-2.3796	0.2671	158	0.235	2626	X-RAY DIFFRACTION	100
2.3796-2.4314	0.2438	146	0.2168	2633	X-RAY DIFFRACTION	99
2.4314-2.4879	0.2602	95	0.2101	2636	X-RAY DIFFRACTION	100
2.4879-2.5502	0.285	110	0.2141	2623	X-RAY DIFFRACTION	100
2.5502-2.6191	0.279	133	0.2132	2635	X-RAY DIFFRACTION	100
2.6191-2.6962	0.2364	160	0.2049	2638	X-RAY DIFFRACTION	100
2.6962-2.7832	0.2544	144	0.1847	2607	X-RAY DIFFRACTION	100
2.7832-2.8827	0.2187	140	0.1898	2616	X-RAY DIFFRACTION	100
2.8827-2.9981	0.2246	144	0.2009	2614	X-RAY DIFFRACTION	100
2.9981-3.1345	0.2265	154	0.201	2614	X-RAY DIFFRACTION	100
3.1345-3.2998	0.1737	144	0.178	2607	X-RAY DIFFRACTION	100
3.2998-3.5065	0.2214	176	0.1731	2577	X-RAY DIFFRACTION	100
3.5065-3.7772	0.1956	141	0.1581	2619	X-RAY DIFFRACTION	100
3.7772-4.1572	0.1865	95	0.1404	2662	X-RAY DIFFRACTION	100
4.1572-4.7586	0.1466	176	0.1369	2588	X-RAY DIFFRACTION	100
4.7586-5.9945	0.1747	138	0.1627	2574	X-RAY DIFFRACTION	99
5.9945-60.0201	0.1638	144	0.1672	2616	X-RAY DIFFRACTION	100

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	0.6843	0.0988	0.8283	0.0246	0.1313	1.0673	-0.1015	-0.2543	0.2777	0.2024	0.0879	0.0886	-0.1558	-0.4228	0.0089	0.3651	0.0327	0.0885	0.1899	-0.0123	0.3369	-21.5103	38.6746	-1.2088
2	0.3329	0.0157	-0.0531	0.325	0.0122	0.2649	0.2965	-0.0891	0.4172	0.1193	-0.1195	0.0756	-0.4907	0.1072	0.013	0.3526	0.041	0.0622	0.2448	-0.0075	0.2888	-15.592	36.6122	-8.7503
3	0.1966	0.2172	-0.1123	0.4011	0.1776	0.4356	0.1155	-0.097	-0.0026	-0.0258	-0.0433	-0.0593	-0.1966	0.1405	0.0044	0.2271	-0.02	0.0097	0.1813	-0.027	0.2026	-5.0804	29.7981	-5.5261
4	0.5921	0.1896	-0.0647	0.3035	0.195	0.1339	0.0583	-0.5317	-0.462	-0.0142	-0.2262	-0.0194	0.1893	0.0772	-0.0005	0.3573	-0.0097	0.0024	0.3995	0.1043	0.3394	-2.2079	6.7223	-4.8323
5	0.0375	0.0344	-0.0335	0.0731	0.0255	0.0854	0.0651	-0.2537	0.0467	-0.0605	0.0095	0.2241	0.3216	-0.0759	0	0.2756	-0.0511	0.0129	0.2363	0.0339	0.2899	-7.5018	9.4129	-6.195
6	0.5081	-0.367	-0.1995	0.3254	0.0724	0.2215	0.2453	-0.1928	0.0893	0.1209	-0.095	-0.0564	0.0071	0.2198	0.0007	0.217	-0.0322	-0.0263	0.2766	0.0116	0.2543	7.1047	19.454	-6.3752
7	1.0394	-0.4028	-0.416	0.2758	0.3191	0.5115	0.1607	-0.0107	0.1338	-0.0164	-0.1071	-0.1658	-0.03	0.0965	-0	0.256	-0.0523	0.0036	0.1911	0.0067	0.2388	-0.2112	26.6637	-9.8999
8	1.2462	-0.1227	-0.2818	0.1075	0.1011	0.0437	0.1211	-0.0649	-0.0313	0.0818	-0.0973	0.1406	-0.1424	-0.0608	0	0.2289	0.0004	0.0241	0.2206	-0.0089	0.2101	-16.3749	26.7654	-6.0068
9	0.2808	0.0621	-0.1095	0.1505	-0.1592	0.2156	0.2682	0.0791	-0.2281	0.169	-0.4263	0.3555	0.7541	-0.9288	-0.0201	0.4019	-0.3038	0.1099	0.8602	-0.117	0.7171	-32.4085	-5.1448	-23.7102
10	0.6273	-0.0067	-0.025	0.3596	-0.2833	0.2462	-0.3695	-0.0367	-0.1358	0.3296	-0.199	0.1851	0.5305	-0.6641	-0.1794	0.3772	-0.1006	0.0279	0.4266	-0.1253	0.4259	-22.9888	-2.7485	-24.2722
11	0.9737	-0.5085	-0.0609	0.8536	0.4736	0.6836	0.188	0.2899	-0.1567	-0.157	-0.3748	0.1412	-0.026	-0.5595	-0.0556	0.2399	-0.075	-0.051	0.3256	-0.1412	0.2413	-19.9326	4.3941	-34.7512
12	0.5444	0.0641	-0.2174	0.1407	-0.0267	0.5131	0.2231	0.4129	0.9968	-0.4688	-0.2716	-0.0824	-0.3653	0.0498	0.0491	0.4356	0.1424	-0.1413	0.2963	0	0.3928	-19.5612	27.627	-37.2711
13	0.1902	0.1504	-0.1229	0.1352	-0.1392	0.1069	0.1582	-0.0338	0.1376	0.1307	-0.2809	0.5688	-0.5007	-0.2631	-0.0181	0.3708	0.1633	-0.0561	0.3299	-0.0978	0.4301	-21.4064	24.7258	-32.0747
14	0.4889	0.1487	-0.0706	0.1501	0.1767	0.1777	-0.0577	0.4408	-0.2291	-0.3475	-0.1881	0.1179	-0.3657	-0.057	-0.0013	0.4304	0.0649	-0.0288	0.3723	0.0172	0.2701	-12.7809	15.5249	-44.3158
15	0.435	0.3143	-0.1587	0.2128	-0.0355	0.1879	0.1691	0.4092	-0.203	-0.5203	-0.2941	0.1281	-0.0636	-0.2244	-0.0001	0.4226	0.0962	-0.0717	0.3882	-0.0815	0.3064	-18.5771	7.3387	-44.7739
16	0.1251	0.1884	-0.0833	0.2425	-0.0226	0.2159	-0.0773	0.2115	-0.5124	-0.0824	-0.0311	-0.2699	0.1998	0.0887	0.0018	0.3155	0.0109	-0.0007	0.2484	-0.0408	0.338	-10.6604	3.9496	-30.5695
17	0.7846	0.1857	-0.5251	0.7402	0.6233	1.069	0.0894	0.0624	0.0016	-0.0039	-0.2513	0.1895	-0.0662	-0.3116	-0.0052	0.1854	0.0166	-0.0234	0.3426	-0.0652	0.2618	-21.3254	9.1354	-26.9613
18	0.1721	0.126	0.1191	0.468	0.5254	1.1631	0.0636	-0.3308	-0.081	0.1585	-0.2458	0.7415	-0.1973	-0.9503	-0.1216	0.2359	-0.1063	0.0611	0.8076	-0.1738	0.5134	-30.6222	5.2573	-20.8303

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 25 through 38 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 39 through 52 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 53 through 83 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 84 through 105 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 106 through 119 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 120 through 142 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 143 through 194 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 195 through 265 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 25 through 38 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 39 through 52 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 53 through 83 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 84 through 105 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 106 through 119 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 120 through 141 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 142 through 165 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 166 through 184 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 185 through 243 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 244 through 265 )

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