PDB-4y0t: Crystal structure of apo form of OXA-58, a Carbapenem hydrolyzing...

ID or keywords:

Entry

Database: PDB / ID: 4y0t

Title

Crystal structure of apo form of OXA-58, a Carbapenem hydrolyzing Class D beta-lactamase from Acinetobacter baumanii (P21, 4mol/ASU)

Components

Beta-lactamase

Keywords

HYDROLASE / Class D beta-lactamase / OXA-58 / 4mol/ASU

Function / homology

Function and homology information

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

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION / Resolution: 2.3 Å

Authors

Pratap, S. / Katiki, M. / Gill, P. / Golemi-Kotra, D. / Kumar, P.

Citation

Journal: Antimicrob.Agents Chemother. / Year: 2015
Title: Active-Site Plasticity Is Essential to Carbapenem Hydrolysis by OXA-58 Class D beta-Lactamase of Acinetobacter baumannii.
Authors: Pratap, S. / Katiki, M. / Gill, P. / Kumar, P. / Golemi-Kotra, D.

History

Deposition	Feb 6, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jan 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 9, 2025	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_ncs_dom_lim Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4y0t.cif.gz	400.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4y0t_validation.pdf.gz	451.1 KB	Display	wwPDB validaton report
Full document	4y0t_full_validation.pdf.gz	453.9 KB	Display
Data in XML	4y0t_validation.xml.gz	38.6 KB	Display
Data in CIF	4y0t_validation.cif.gz	54.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y0/4y0t ftp://data.pdbj.org/pub/pdb/validation_reports/y0/4y0t	HTTPS FTP

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Related structure data

Related structure data	4y0oC 4y0uC C: citing same article (ref.)
Similar structure data	4y0u-4 4y0o-d 5kzh-2 5cxr-d 6pt5-4 1pzp-d 5i52-1 1nyy-d 4y0u-1 6t1h-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

4y0oC

4y0uC

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	#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) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

C: Beta-lactamase

D: Beta-lactamase

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

1

A: Beta-lactamase

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

2

B: Beta-lactamase

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

3

C: Beta-lactamase

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

4

D: Beta-lactamase

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

Unit cell

Length a, b, c (Å)	37.017, 65.095, 191.964
Angle α, β, γ (deg.)	90.00, 91.28, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	D
1	2	A
2	2	D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	KCX	KCX	A	A	38 - 86	38 - 86
2	1	SER	SER	KCX	KCX	D	D	38 - 86	38 - 86
1	2	ILE	ILE	TYR	TYR	A	A	87 - 279	87 - 279
2	2	ILE	ILE	TYR	TYR	D	D	87 - 279	87 - 279

NCS ensembles :

ID
1
2

#1: Protein	Beta-lactamase Mass: 31498.209 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaOXA-58, bla-oxa-58, bla-oxa58 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2TR58, beta-lactamase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.84 Å³/Da / Density % sol: 32.98 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris base/Hydrochloric acid (pH 8.0) and 28% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 4, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.29→34.79 Å / Num. obs: 37470 / % possible obs: 91.23 % / Redundancy: 2.8 % / R_merge(I) obs: 0.12 / Net I/σ(I): 9.15
Reflection shell	Resolution: 2.29→2.37 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.42 / % possible all: 74.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Resolution: 2.3→34.79 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.933 / SU B: 20.364 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.765 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24328	1847	4.9 %	RANDOM
R_work	0.19414	-	-	-
obs	0.19651	35622	91.21 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 44.466 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.05 Å²	0 Å²	-0.54 Å²
2-	-	0.87 Å²	0 Å²
3-	-	-	-0.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→34.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7740	0	0	388	8128

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	7934
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	7601
X-RAY DIFFRACTION	r_angle_refined_deg	1.675	1.947	10720
X-RAY DIFFRACTION	r_angle_other_deg	1.349	3	17462
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.607	5	967
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.648	24.883	383
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.764	15	1370
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.144	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	1151
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	9016
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1880
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	1.189	1.893	3868
X-RAY DIFFRACTION	r_mcbond_other	1.188	1.893	3867
X-RAY DIFFRACTION	r_mcangle_it	1.984	2.836	4825
X-RAY DIFFRACTION	r_mcangle_other	1.984	2.836	4826
X-RAY DIFFRACTION	r_scbond_it	1.334	2.007	4066
X-RAY DIFFRACTION	r_scbond_other	1.334	2.007	4067
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.229	2.954	5893
X-RAY DIFFRACTION	r_long_range_B_refined	4.936	15.414	9128
X-RAY DIFFRACTION	r_long_range_B_other	4.906	15.24	9063
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 2460 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	D

LS refinement shell

Resolution: 2.296→2.355 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.411	84	-
R_work	0.305	1837	-
obs	-	-	63.84 %

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	2.6606	-0.6961	1.328	1.6075	-0.9722	3.94	0.0301	-0.0281	0.2071	0.1664	-0.0654	-0.063	-0.0698	0.2254	0.0353	0.049	-0.018	0.051	0.3309	0.0022	0.1095	-3.1	1.303	74.161
2	4.8326	1.3668	-0.6863	8.0397	0.9421	4.6139	0.0941	0.1894	-0.5276	0.0042	0.0063	0.0617	0.5876	-0.0052	-0.1004	0.1276	0.0172	-0.0044	0.4463	-0.0093	0.1286	-14.85	-7.627	53.66
3	2.1453	-0.477	0.3923	1.9704	-1.3979	2.9114	0.0729	0.0239	0.0351	-0.0216	0.0039	0.0016	0.0245	-0.075	-0.0768	0.0154	-0.019	0.0004	0.396	-0.0199	0.0611	-8.305	0.945	69.313
4	7.9182	3.991	2.2289	4.4199	-0.0365	11.4989	0.0232	0.3205	-0.2254	-0.2917	-0.0271	-0.5231	0.1196	0.0028	0.004	0.213	0.0321	0.016	0.4085	0.011	0.2075	-59.671	56.792	37.616
5	4.5376	1.2367	-1.6667	2.2627	-0.7323	3.1015	-0.1979	0.1216	-0.1951	-0.1384	0.0883	-0.288	0.051	0.3381	0.1097	0.0429	0.0433	0.0041	0.3729	0.0041	0.1168	-59.645	53.169	24.206
6	2.4084	-0.7224	0.1356	0.8431	1.1359	2.4107	-0.1407	0.2069	-0.0361	0.1193	-0.039	0.103	0.1416	-0.2673	0.1797	0.1347	-0.0282	0.0272	0.5629	-0.0108	0.0173	-43.148	56.657	5.629
7	7.1361	4.3575	2.6184	8.6524	0.5018	3.5679	-0.3768	-0.563	1.1415	0.567	-0.3198	-0.3662	-0.6117	-0.2071	0.6966	0.2208	0.0819	-0.1587	0.4668	-0.0045	0.5624	-42.653	74.04	4.202
8	2.7678	-0.5086	-0.9385	3.2817	0.6213	2.0029	-0.1832	-0.1411	0.0274	0.087	0.057	-0.065	0.0326	0.0887	0.1262	0.1096	0.004	-0.015	0.3755	-0.0109	0.0211	-47.846	57.761	3.658
9	4.0104	-1.687	-2.43	2.7775	-0.5132	7.1661	-0.1462	-0.2022	0.3016	0.2479	0.0146	-0.2745	-0.135	0.2833	0.1316	0.0677	-0.004	-0.0364	0.3549	0.0052	0.0943	-56.764	57.403	6.345
10	9.0772	-0.2117	-3.6892	3.1404	0.8311	6.8845	-0.2367	0.1907	-0.3592	0.1322	-0.0656	0.0315	0.5032	-0.1502	0.3022	0.1624	-0.0341	0.0089	0.3221	-0.0167	0.0405	-41.927	48.334	14.493
11	5.5558	0.4761	-0.7823	2.4724	-0.8134	0.4522	-0.1443	0.2426	0.2425	0.0904	0.1138	0.088	-0.0827	-0.0597	0.0305	0.104	-0.0043	-0.0111	0.3743	0.0171	0.1187	-46.28	60.186	20.803
12	3.4336	2.2518	-1.0053	6.7214	1.3738	3.4327	-0.3598	-0.1768	0.1771	-0.4143	0.0953	-0.1772	-0.522	0.0569	0.2644	0.1844	0.0323	-0.0968	0.3676	0.0672	0.1554	-54.039	61.183	23.523
13	6.1001	3.6936	5.4349	3.6264	1.0066	8.7213	-0.4577	0.1208	0.3591	-0.3124	0.1759	0.1369	-0.4417	-0.1026	0.2817	0.1272	0.0801	0.1077	0.5032	0.0829	0.2608	-49.938	61.461	31.926

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	38 - 101
2	X-RAY DIFFRACTION	2	A	102 - 141
3	X-RAY DIFFRACTION	3	A	142 - 279
4	X-RAY DIFFRACTION	4	D	38 - 50
5	X-RAY DIFFRACTION	5	D	51 - 81
6	X-RAY DIFFRACTION	6	D	82 - 101
7	X-RAY DIFFRACTION	7	D	102 - 121
8	X-RAY DIFFRACTION	8	D	122 - 161
9	X-RAY DIFFRACTION	9	D	162 - 181
10	X-RAY DIFFRACTION	10	D	182 - 201
11	X-RAY DIFFRACTION	11	D	202 - 241
12	X-RAY DIFFRACTION	12	D	242 - 261
13	X-RAY DIFFRACTION	13	D	262 - 279

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