PDB-6nhu: Crystal Structure of the Beta Lactamase Class D YbxI from Agrobac...

ID or keywords:

Entry

Database: PDB / ID: 6nhu

Title

Crystal Structure of the Beta Lactamase Class D YbxI from Agrobacterium fabrum

Components

Beta-lactamase

Keywords

HYDROLASE / beta lactamase class D / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function

Biological species

Agrobacterium fabrum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Kim, Y. / Welk, L. / Endres, M. / Babnigg, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of the Beta Lactamase Class D YbxI from Agrobacterium fabrum
Authors: Kim, Y. / Welk, L. / Endres, M. / Babnigg, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Dec 23, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 16, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 11, 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	6nhu.cif.gz	388 KB	Display	PDBx/mmCIF format
PDB format	pdb6nhu.ent.gz	320.7 KB	Display	PDB format
PDBx/mmJSON format	6nhu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6nhu_validation.pdf.gz	480.9 KB	Display	wwPDB validaton report
Full document	6nhu_full_validation.pdf.gz	486.4 KB	Display
Data in XML	6nhu_validation.xml.gz	35.1 KB	Display
Data in CIF	6nhu_validation.cif.gz	47.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nh/6nhu ftp://data.pdbj.org/pub/pdb/validation_reports/nh/6nhu	HTTPS FTP

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Related structure data

Related structure data	4gn2S S: Starting model for refinement
Similar structure data	5l9e-d 1lmk-d 4fu4-d 2azt-1 3zh8-d 5gmr-d 3qs7-2 2g5c-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
Other databases	TargetTrack: CSGID-IDP97205

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

C: Beta-lactamase

D: Beta-lactamase

hetero molecules

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

1

Idetical with deposited unit
defined by author

2

A: Beta-lactamase

C: Beta-lactamase

hetero molecules

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

3

B: Beta-lactamase

D: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.879, 165.957, 75.428
Angle α, β, γ (deg.)	90.00, 90.02, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase Mass: 27888.381 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Strain: C58 / ATCC 33970 / Gene: Atu0933 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7D0B8, beta-lactamase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.8 Å³/Da / Density % sol: 56.05 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 0.04 M potassium phosphate, 16 %(w/v) PEG8000, 20 % glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 19, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 54045 / % possible obs: 97.3 % / Redundancy: 4.4 % / CC_1/2: 0.956 / R_merge(I) obs: 0.16 / Net I/σ(I): 14
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.706 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2266 / CC_1/2: 0.597 / % possible all: 83.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDBID 4GN2

4gn2

Resolution: 2.3→44.608 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.74

	R_factor	Num. reflection	% reflection
R_free	0.2227	2673	4.96 %
R_work	0.187	-	-
obs	0.1888	53884	96.83 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 46 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→44.608 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7594	0	32	114	7740

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7833
X-RAY DIFFRACTION	f_angle_d	0.573	10636
X-RAY DIFFRACTION	f_dihedral_angle_d	18.154	4635
X-RAY DIFFRACTION	f_chiral_restr	0.042	1115
X-RAY DIFFRACTION	f_plane_restr	0.005	1405

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 (%)
2.281-2.3225	0.2808	91	0.2608	2093	X-RAY DIFFRACTION	76
2.3225-2.3671	0.2554	158	0.2222	2741	X-RAY DIFFRACTION	97
2.3671-2.4154	0.2861	147	0.2216	2678	X-RAY DIFFRACTION	98
2.4154-2.468	0.2548	121	0.2225	2744	X-RAY DIFFRACTION	98
2.468-2.5254	0.2484	137	0.2285	2765	X-RAY DIFFRACTION	98
2.5254-2.5885	0.3027	146	0.2191	2747	X-RAY DIFFRACTION	99
2.5885-2.6585	0.2822	160	0.2243	2727	X-RAY DIFFRACTION	99
2.6585-2.7367	0.2849	146	0.2233	2648	X-RAY DIFFRACTION	96
2.7367-2.825	0.2767	128	0.2293	2686	X-RAY DIFFRACTION	98
2.825-2.926	0.2672	117	0.2203	2799	X-RAY DIFFRACTION	99
2.926-3.0431	0.2556	143	0.2121	2718	X-RAY DIFFRACTION	99
3.0431-3.1816	0.2757	142	0.2223	2746	X-RAY DIFFRACTION	99
3.1816-3.3493	0.2453	134	0.2077	2790	X-RAY DIFFRACTION	99
3.3493-3.559	0.2416	154	0.1963	2679	X-RAY DIFFRACTION	97
3.559-3.8337	0.2395	149	0.1857	2701	X-RAY DIFFRACTION	98
3.8337-4.2192	0.1724	117	0.1572	2794	X-RAY DIFFRACTION	99
4.2192-4.8291	0.1769	159	0.1355	2742	X-RAY DIFFRACTION	98
4.8291-6.0817	0.2034	146	0.1589	2692	X-RAY DIFFRACTION	97
6.0817-44.6166	0.1596	178	0.1619	2721	X-RAY DIFFRACTION	97

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	0.2853	-0.3288	0.3314	0.3145	-0.323	0.1826	0.1082	-0.0091	0.3202	0.0534	0.0826	0.2613	-0.1218	-0.3247	0.0015	0.2822	-0.0198	-0.0843	0.3524	-0.0111	0.3666	10.8439	0.7074	23.126
2	0.562	-0.374	0.2779	0.2245	-0.0253	0.3999	-0.0653	0.1661	-0.0769	0.2966	0.0611	-0.076	0.1462	-0.0458	-0	0.3504	0.0584	-0.0878	0.2649	-0.0218	0.3011	26.6375	1.3067	45.6304
3	0.7614	0.9413	-0.1514	1.2158	-0.4568	0.3755	-0.0022	-0.0872	0.0507	0.2864	0.0242	-0.2496	0.0061	-0.0152	-0	0.363	0.0191	-0.0344	0.3233	-0.0539	0.302	23.7653	-0.5923	45.6544
4	1.2293	-0.229	0.0222	1.4282	0.1348	0.8429	-0.0274	-0.0185	0.0335	0.1497	-0.0022	0.0128	-0.1524	-0.11	0	0.2949	0.0164	-0.0196	0.3147	-0.0021	0.3054	17.7691	2.9825	35.7031
5	0.9591	-0.7431	0.592	0.6141	-0.2249	0.3988	-0.1526	-0.0952	-0.1511	-0.351	0.1537	0.4322	0.2347	0.0122	-0.0006	0.3274	-0.0047	-0.0131	0.303	-0.0108	0.3591	14.0375	-10.4584	33.9449
6	1.0634	-0.4322	0.337	0.221	-0.1462	0.5478	0.0415	0.1986	-0.222	-0.2236	0.0287	-0.5953	0.1825	0.1051	-0	0.2297	0.0047	-0.0187	0.2822	-0.0175	0.306	19.139	-4.6726	23.7229
7	0.2208	0.2592	-0.1444	0.2865	-0.0626	0.1251	0.0706	0.4464	-0.3946	-0.9289	0.1148	-0.3701	0.7198	0.0214	-0.0006	0.421	0.045	0.0065	0.4372	-0.021	0.4404	22.3786	-4.5156	19.5348
8	0.3489	-0.3115	-0.2671	0.413	0.4233	0.1504	-0.0411	0.0552	-0.1545	0.0334	-0.0894	-0.0112	0.1612	0.2345	-0.0005	0.2953	-0.0024	0.0824	0.3494	-0.0041	0.3953	63.9597	-32.9818	60.8861
9	1.4468	0.1664	-0.6838	2.2657	0.1709	0.899	-0.0127	-0.1137	-0.0665	0.3288	0.0169	0.0391	0.0253	0.0807	-0	0.3127	0.0269	0.023	0.2907	0.021	0.2327	53.8508	-33.9452	80.5178
10	0.8295	-0.8673	-0.5655	1.1131	0.0653	0.5981	-0.0274	-0.0848	0.1969	0.062	-0.0166	0.1234	-0.0996	-0.1619	-0	0.2796	-0.0034	0.0157	0.3386	0.0129	0.3066	55.4481	-26.1529	67.3489
11	1.6562	-0.3203	0.0889	0.3224	0.3313	0.5293	0.1187	-0.0338	0.1194	-0.4931	-0.0399	0.3937	-0.2071	-0.2001	-0	0.3319	0.0069	0.0016	0.3503	0.0367	0.3432	54.4204	-27.0755	59.8934
12	0.2985	-0.2774	-0.5679	0.8981	0.1993	0.9454	-0.1312	-0.1503	-0.1962	0.1885	-0.0489	0.1598	0.1625	0.0732	0	0.2801	-0.0306	0.0588	0.2967	-0.0224	0.2632	25.4313	-38.083	44.2446
13	0.8295	0.7339	-1.0976	0.8112	-0.3213	1.4398	0.0137	0.1826	0.0928	-0.2094	-0.0232	-0.1869	0.1744	0.039	0	0.3695	0.0172	0.0648	0.378	-0.0158	0.3194	39.0042	-40.5476	27.0482
14	1.5854	-0.1677	-0.4157	0.8407	-0.1965	1.3087	-0.1254	-0.1561	-0.0482	0.0154	0.041	-0.0573	0.0806	0.0279	-0	0.2787	-0.0103	0.0164	0.2598	0.005	0.2671	31.8912	-38.6793	39.4732
15	0.8638	-0.4148	-0.7354	0.7844	-0.2424	1.3652	-0.0075	0.0959	-0.3132	-0.1875	-0.0263	-0.2521	0.1126	-0.4444	-0.0076	0.2814	-0.0707	0.0235	0.3306	-0.024	0.3292	19.6818	-39.6637	37.2041
16	0.1979	0.1078	-0.0469	0.2843	-0.0581	-0.0017	-0.2126	0.4853	0.4343	0.0515	-0.1985	0.3754	-0.0105	-0.2983	-0.0003	0.3992	0.0168	-0.0105	0.3255	0.0007	0.358	16.8531	-28.1666	39.1754
17	0.102	0.2879	0.3112	0.4111	-0.1849	0.5872	-0.1461	-0.0778	0.1947	0.1176	-0.0253	-0.0189	-0.2285	-0.0658	-0.0001	0.2566	-0.019	-0.0612	0.2511	0.009	0.2567	49.3461	5.8806	81.9693
18	0.5478	-0.0834	0.0991	0.3611	0.4421	0.8411	-0.0817	0.185	-0.0703	-0.3049	0.0729	-0.0444	0.291	0.1011	0.0001	0.324	-0.0016	-0.0763	0.3398	-0.0205	0.3345	37.1209	4.6772	60.4629
19	0.5558	0.3634	0.3058	0.7497	0.0316	0.1787	-0.1725	0.1579	0.0178	-0.094	-0.1834	0.4465	-0.3728	-0.2088	-0.0001	0.3237	0.0697	-0.043	0.3865	-0.0058	0.3832	33.6105	13.9701	71.052
20	0.2906	0.2465	-0.1612	0.2617	0.0277	0.1865	-0.1084	-0.0392	0.2404	0.1173	0.0818	-0.222	-0.7842	0.4936	0	0.4138	-0.0239	-0.0748	0.2929	0.0327	0.3621	43.1254	19.6306	73.7665
21	0.0246	0.0023	-0.0307	0.0313	-0.0102	0.2116	-0.0236	-1.0363	0.2811	0.2908	-0.1787	0.265	-0.1763	-0.2079	-0.0004	0.2881	0.0338	0.0091	0.3359	-0.0527	0.304	43.7464	4.333	84.865
22	0.1999	-0.1055	-0.1223	0.141	0.1217	0.0773	-0.1635	-0.1525	-0.0521	0.1775	-0.028	0.2029	0.5528	0.1083	-0.0001	0.3287	-0.057	0.008	0.3977	0.0085	0.3416	32.9645	-0.0045	80.3136
23	0.6183	-0.0533	-0.1382	0.2037	0.2108	0.3413	0.1823	0.048	-0.1185	-0.0826	-0.1871	0.0669	0.099	0.2663	0.0001	0.3596	-0.0164	-0.0136	0.2875	0.033	0.3445	50.1834	-4.3776	74.1787
24	0.8305	-0.7027	0.2688	0.4598	-0.0259	1.0825	-0.0362	-0.0365	0.2547	0.2376	0.1095	-0.2519	-0.3454	0.099	-0	0.3069	-0.09	-0.0397	0.301	-0.0159	0.3799	54.1266	11.6449	73.7447
25	0.4086	-0.3244	0.4956	0.5644	-0.0838	0.6225	-0.1569	0.1908	0.0262	-0.1129	0.0284	0.1477	-0.0103	0.1947	-0.0001	0.3395	-0.0577	-0.047	0.4014	0.0246	0.2294	56.1505	2.3587	76.4264
26	0.1207	0.1958	0.131	0.337	0.1365	0.044	-0.5501	0.2657	-0.3049	0.156	0.0905	-0.6737	0.1277	-0.0308	-0.0004	0.4062	0.0166	0.0435	0.3029	0.0051	0.3659	57.8433	-4.3191	76.9377

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 30 through 58 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 92 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 93 through 133 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 134 through 211 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 212 through 233 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 234 through 254 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 255 through 272 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 30 through 58 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 59 through 193 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 194 through 234 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 235 through 272 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 29 through 72 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 73 through 133 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 134 through 211 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 212 through 254 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 255 through 272 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 29 through 72 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 73 through 110 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 111 through 133 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 134 through 162 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 163 through 174 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 175 through 191 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 192 through 211 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 212 through 234 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 235 through 254 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 255 through 272 )

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