PDB-8sq7: X-ray crystal structure of Acinetobacter baumanii beta-lactamase ...

ID or keywords:

Entry

Database: PDB / ID: 8sq7

Title

X-ray crystal structure of Acinetobacter baumanii beta-lactamase variant OXA-82 K83D in complex with doripenem

Components

Beta-lactamase OXA-82

Keywords

HYDROLASE/INHIBITOR / ANTIBIOTIC / Acinetobacter beta-lactamase Complex carbapenem Doripenem / HYDROLASE / HYDROLASE-INHIBITOR / ANTIBIOTIC complex

Function / homology

Function and homology information

penicillin binding / beta-lactamase
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

Powers, R.A. / Leonard, D.A. / June, C.M. / Szarecka, A. / Wawrzak, Z.

Funding support

United States, 1items

Citation

Journal: J.Mol.Biol. / Year: 2024
Title: Structural and Dynamic Features of Acinetobacter baumannii OXA-66 beta-Lactamase Explain Its Stability and Evolution of Novel Variants.
Authors: Klamer, Z.L. / June, C.M. / Wawrzak, Z. / Taracila, M.A. / Grey, J.A. / Benn, A.M.I. / Russell, C.P. / Bonomo, R.A. / Powers, R.A. / Leonard, D.A. / Szarecka, A.

History

Deposition	May 4, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 22, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8sq7.cif.gz	795.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8sq7.ent.gz	661.8 KB	Display	PDB format
PDBx/mmJSON format	8sq7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8sq7_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	8sq7_full_validation.pdf.gz	2.9 MB	Display
Data in XML	8sq7_validation.xml.gz	88 KB	Display
Data in CIF	8sq7_validation.cif.gz	122.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sq/8sq7 ftp://data.pdbj.org/pub/pdb/validation_reports/sq/8sq7	HTTPS FTP

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Related structure data

Related structure data	8sq8C C: citing same article (ref.)
Similar structure data	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	#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) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

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)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

Deposited unit

A: Beta-lactamase OXA-82

B: Beta-lactamase OXA-82

C: Beta-lactamase OXA-82

D: Beta-lactamase OXA-82

E: Beta-lactamase OXA-82

F: Beta-lactamase OXA-82

G: Beta-lactamase OXA-82

H: Beta-lactamase OXA-82

hetero molecules

229 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-lactamase OXA-82

hetero molecules

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

2

B: Beta-lactamase OXA-82

hetero molecules

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

3

C: Beta-lactamase OXA-82

hetero molecules

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

4

D: Beta-lactamase OXA-82

hetero molecules

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

5

E: Beta-lactamase OXA-82

hetero molecules

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

6

F: Beta-lactamase OXA-82

hetero molecules

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

7

G: Beta-lactamase OXA-82

hetero molecules

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

8

H: Beta-lactamase OXA-82

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.284, 70.284, 448.355
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

#1: Protein	Beta-lactamase OXA-82 Mass: 28067.975 Da / Num. of mol.: 8 / Mutation: K83D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: bla-OXA-82, blaOXA-82, oxa66 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / References: UniProt: A8HDA9
#2: Chemical	ChemComp-4J6 / (4R,5S)-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-3-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-4,5-dihydro-1H-pyrrole-2-carboxylic acid / Doripenem(open form, pyrroline tautomer form 1, SP2 connection to Thio) Mass: 422.520 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₅H₂₆N₄O₆S₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₅O₇
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1501 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.85 Å³/Da / Density % sol: 56.8 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.09 M HEPES, pH 7.5, 1.26 M Sodium Citrate, 10% v/v glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 30, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9787 Å / Relative weight: 1
Reflection	Resolution: 1.78→50 Å / Num. obs: 235628 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC_1/2: 0.976 / Net I/σ(I): 34.2
Reflection shell	Resolution: 1.78→1.84 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 23812 / CC_1/2: 0.873 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.78→38.58 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.954 / SU B: 4.531 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18098	10377	5 %	RANDOM
R_work	0.1546	-	-	-
obs	0.15591	197119	87.64 %	-

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: 25.989 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.24 Å²	-0.12 Å²	0 Å²
2-	-	-0.24 Å²	0 Å²
3-	-	-	0.79 Å²

Refinement step

Cycle: 1 / Resolution: 1.78→38.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15060	0	310	1501	16871

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	15857
X-RAY DIFFRACTION	r_bond_other_d	0	0.017	14564
X-RAY DIFFRACTION	r_angle_refined_deg	1.329	1.66	21549
X-RAY DIFFRACTION	r_angle_other_deg	1.324	1.594	33890
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.492	5	1952
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.064	24.422	753
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.14	15	2715
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.747	15	53
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	2069
X-RAY DIFFRACTION	r_gen_planes_refined	0.017	0.02	17621
X-RAY DIFFRACTION	r_gen_planes_other	0.01	0.02	3118
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	2.565	0.918	7745
X-RAY DIFFRACTION	r_mcbond_other	2.565	0.918	7746
X-RAY DIFFRACTION	r_mcangle_it	3.261	1.359	9685
X-RAY DIFFRACTION	r_mcangle_other	3.261	1.36	9686
X-RAY DIFFRACTION	r_scbond_it	5.86	1.413	8112
X-RAY DIFFRACTION	r_scbond_other	5.861	1.412	8111
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.261	1.909	11854
X-RAY DIFFRACTION	r_long_range_B_refined	8.683	13.444	18504
X-RAY DIFFRACTION	r_long_range_B_other	8.684	13.447	18505
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	7811	0.07
1	2	B	7811	0.07
2	1	A	8190	0.05
2	2	C	8190	0.05
3	1	A	8207	0.04
3	2	D	8207	0.04
4	1	A	8118	0.04
4	2	E	8118	0.04
5	1	A	7888	0.07
5	2	F	7888	0.07
6	1	A	7815	0.07
6	2	G	7815	0.07
7	1	A	7840	0.08
7	2	H	7840	0.08
8	1	B	7812	0.08
8	2	C	7812	0.08
9	1	B	7832	0.07
9	2	D	7832	0.07
10	1	B	7865	0.08
10	2	E	7865	0.08
11	1	B	8041	0.03
11	2	F	8041	0.03
12	1	B	8066	0.04
12	2	G	8066	0.04
13	1	B	8140	0.03
13	2	H	8140	0.03
14	1	C	8202	0.04
14	2	D	8202	0.04
15	1	C	8096	0.04
15	2	E	8096	0.04
16	1	C	7842	0.08
16	2	F	7842	0.08
17	1	C	7762	0.08
17	2	G	7762	0.08
18	1	C	7786	0.08
18	2	H	7786	0.08
19	1	D	8129	0.03
19	2	E	8129	0.03
20	1	D	7870	0.07
20	2	F	7870	0.07
21	1	D	7787	0.07
21	2	G	7787	0.07
22	1	D	7811	0.08
22	2	H	7811	0.08
23	1	E	7763	0.07
23	2	F	7763	0.07
24	1	E	7795	0.07
24	2	G	7795	0.07
25	1	E	7815	0.08
25	2	H	7815	0.08
26	1	F	7970	0.05
26	2	G	7970	0.05
27	1	F	7988	0.04
27	2	H	7988	0.04
28	1	G	8054	0.04
28	2	H	8054	0.04

LS refinement shell

Resolution: 1.782→1.828 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.262	360	-
R_work	0.218	6653	-
obs	-	-	40.01 %

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	0.8346	0.0302	-0.3478	1.8605	-0.0306	2.8756	0.0697	0.0376	0.057	0.0966	0.0825	0.0962	-0.0384	0.1843	-0.1522	0.1067	0.0086	0.0523	0.0501	0.0106	0.0384	51.101	39.382	1.316
2	1.8304	0.5559	0.9056	1.124	0.1416	2.6461	0.1374	0.3257	-0.115	0.1341	0.0642	-0.1413	0.3221	0.3517	-0.2015	0.1945	0.0235	-0.0376	0.0986	-0.0241	0.0326	77.763	57.17	-10.38
3	1.6794	0.4625	-0.1996	1.0933	0.2162	2.9485	0.1394	-0.0533	0.1049	0.0002	0.0108	-0.0052	0.1491	0.1414	-0.1502	0.0706	-0.0291	0.0359	0.0762	-0.0405	0.0393	59.776	16.029	-73.382
4	1.7391	0.4968	0.1045	1.1628	-0.3186	2.9576	0.0205	0.069	0.0478	0.0167	0.1272	0.0952	0.1872	0.0629	-0.1478	0.048	-0.0156	-0.0171	0.0926	0.049	0.0377	61.762	57.755	-48.589
5	0.8024	-0.0336	0.3741	1.8339	-0.0212	2.8896	0.0719	-0.0272	-0.0517	-0.0983	0.0776	0.1044	0.0353	0.1826	-0.1495	0.1071	-0.0096	-0.0517	0.0486	0.0099	0.0373	86.295	62.048	26.052
6	1.8972	-0.558	-0.9585	1.115	0.1598	2.6558	0.1424	-0.3422	0.1169	-0.127	0.0664	-0.1447	-0.3304	0.3726	-0.2087	0.1973	-0.0279	0.0365	0.1052	-0.025	0.0349	42.751	44.299	37.978
7	0.8162	-0.0266	-0.3232	2.1709	0.8577	2.6624	-0.1139	-0.0188	-0.0594	0.1913	0.3164	-0.1775	0.1489	0.4512	-0.2025	0.1024	-0.0294	-0.0036	0.19	-0.0442	0.0325	59.564	25.832	-36.828
8	1.7861	-0.6314	0.5998	1.214	-0.7799	2.6953	0.2876	-0.0373	-0.1828	-0.2532	-0.0819	0.0356	0.4759	-0.0993	-0.2057	0.1471	-0.0546	-0.0391	0.152	0.0196	0.0346	53.214	62.658	-85.239

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	34 - 274
2	X-RAY DIFFRACTION	2	B	35 - 274
3	X-RAY DIFFRACTION	3	C	34 - 274
4	X-RAY DIFFRACTION	4	D	34 - 274
5	X-RAY DIFFRACTION	5	E	35 - 274
6	X-RAY DIFFRACTION	6	F	35 - 274
7	X-RAY DIFFRACTION	7	G	35 - 274
8	X-RAY DIFFRACTION	8	H	35 - 274

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