PDB-7o9n: Crystal Structure of a Class D Carbapenemase Complexed with Bicar...

ID or keywords:

Entry

Database: PDB / ID: 7o9n

Title

Crystal Structure of a Class D Carbapenemase Complexed with Bicarbonate

Components

Beta-lactamase

Keywords

HYDROLASE / OXA / Bicarbonate

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 /

MOLECULAR REPLACEMENT / Resolution: 1.97 Å

Authors

Zhou, Q. / He, Y. / Jin, Y.

Funding support

China, 1items

Citation

Journal: Acs Cent.Sci. / Year: 2023
Title: An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity
Authors: Zhou, Q. / Catalan, P. / Bell, H. / Baumann, P. / Cooke, R. / Evans, R. / Yang, J. / Zhang, Z. / Zappala, D. / Zhang, Y. / Blackburn, G.M. / He, Y. / Jin, Y.

History

Deposition	Apr 16, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 4, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
Revision 1.2	Mar 6, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7o9n.cif.gz	748.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7o9n.ent.gz		Display	PDB format
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Validation report

Summary document	7o9n_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	7o9n_full_validation.pdf.gz	1.6 MB	Display
Data in XML	7o9n_validation.xml.gz	41.9 KB	Display
Data in CIF	7o9n_validation.cif.gz	59.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o9/7o9n ftp://data.pdbj.org/pub/pdb/validation_reports/o9/7o9n	HTTPS FTP

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Related structure data

Related structure data	7nrjC 7o5nC 7o5tC 7pehC 7peiC 7pepC 7pfnC 7pgoC 7pseC 7psfC 7q14C 4s2pS S: Starting model for refinement 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	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #59 - Nov 2004 Photosystem II similarity (1)

Deposited unit

AAA: Beta-lactamase

BBB: Beta-lactamase

CCC: Beta-lactamase

DDD: Beta-lactamase

hetero molecules

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

1

AAA: Beta-lactamase

DDD: Beta-lactamase

hetero molecules

defined by author
Evidence: gel filtration
60.7 kDa, 2 polymers

2

BBB: Beta-lactamase

CCC: Beta-lactamase

hetero molecules

defined by author
60.6 kDa, 2 polymers

Unit cell

Length a, b, c (Å)	81.807, 106.404, 124.706
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	AAA
6	3	DDD
7	4	BBB
8	4	CCC
9	5	BBB
10	5	DDD
11	6	CCC
12	6	DDD

NCS domain segments:

End auth comp-ID: ILE / End label comp-ID: ILE

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	AAA	A	22 - 264	17 - 259
2	2	1	GLY	GLY	BBB	B	22 - 264	17 - 259
3	1	2	GLY	GLY	AAA	A	22 - 264	17 - 259
4	2	2	GLY	GLY	CCC	C	22 - 264	17 - 259
5	1	3	LYS	LYS	AAA	A	23 - 264	18 - 259
6	2	3	LYS	LYS	DDD	D	23 - 264	18 - 259
7	1	4	GLN	GLN	BBB	B	21 - 264	16 - 259
8	2	4	GLN	GLN	CCC	C	21 - 264	16 - 259
9	1	5	LYS	LYS	BBB	B	23 - 264	18 - 259
10	2	5	LYS	LYS	DDD	D	23 - 264	18 - 259
11	1	6	LYS	LYS	CCC	C	23 - 264	18 - 259
12	2	6	LYS	LYS	DDD	D	23 - 264	18 - 259

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Beta-lactamase Mass: 30254.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: bla OXA-48, bla_2, blaOXA-48, G5637_27540, KPE71T_00045, SAMEA3649466_05396 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical	ChemComp-BCT / BICARBONATE ION Mass: 61.017 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CHO₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 612 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.24 Å³/Da / Density % sol: 45.15 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 11.6% PEG8000, 8% 1-BuOH, mixed with the 10 mg/mL protein stock at 1:1 ratio.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 14, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976254 Å / Relative weight: 1
Reflection	Resolution: 1.97→81.81 Å / Num. obs: 77632 / % possible obs: 100 % / Redundancy: 13.2 % / CC_1/2: 0.995 / Net I/σ(I): 6
Reflection shell	Resolution: 1.97→2.01 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4552 / CC_1/2: 0.582

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
xia2		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4S2P

4s2p

Resolution: 1.97→68.496 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.887 / SU B: 16.454 / SU ML: 0.191 / Cross valid method: FREE R-VALUE / ESU R Free: 0.197
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2861	3748	4.834 %
R_work	0.1954	73791	-
all	0.2	-	-
obs	-	77539	99.981 %

Solvent computation

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

Displacement parameters

B_iso mean: 25.536 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.123 Å²	-0 Å²	-0 Å²
2-	-	-0.957 Å²	0 Å²
3-	-	-	2.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.97→68.496 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8029	0	20	614	8663

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	8270
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.018	7711
X-RAY DIFFRACTION	r_angle_refined_deg	1.466	1.633	11185
X-RAY DIFFRACTION	r_angle_other_deg	1.327	1.586	17690
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.494	5	982
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.024	22.908	478
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.572	15	1442
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.049	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	1036
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	9502
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2070
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1685
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	7334
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	3975
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	3641
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.184	0.2	487
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.055	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.314	0.2	38
X-RAY DIFFRACTION	r_nbd_other	0.249	0.2	96
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.148	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	4.215	2.513	3928
X-RAY DIFFRACTION	r_mcbond_other	4.209	2.513	3927
X-RAY DIFFRACTION	r_mcangle_it	5.295	3.782	4907
X-RAY DIFFRACTION	r_mcangle_other	5.294	3.783	4908
X-RAY DIFFRACTION	r_scbond_it	4.803	2.786	4342
X-RAY DIFFRACTION	r_scbond_other	4.798	2.785	4339
X-RAY DIFFRACTION	r_scangle_it	5.806	4.079	6277
X-RAY DIFFRACTION	r_scangle_other	5.793	4.078	6274
X-RAY DIFFRACTION	r_lrange_it	6.67	29.317	9677
X-RAY DIFFRACTION	r_lrange_other	6.582	29.171	9566
X-RAY DIFFRACTION	r_rigid_bond_restr	9.944	3	15981
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.045	0.05	8546
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.072	0.05	8403
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.066	0.05	8436
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.072	0.05	8464
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.064	0.05	8497
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.057	0.05	8503

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.04488	0.0501
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.04488	0.0501
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.07171	0.05009
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.07171	0.05009
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.06577	0.05009
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.06577	0.05009
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.07196	0.05009
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.07196	0.05009
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.06384	0.05009
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.06384	0.05009
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.05701	0.05009
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.05701	0.05009

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 (%)
1.97-2.021	0.356	267	0.315	5383	X-RAY DIFFRACTION	100
2.021-2.077	0.394	231	0.305	5296	X-RAY DIFFRACTION	100
2.077-2.137	0.351	260	0.265	5111	X-RAY DIFFRACTION	99.9814
2.137-2.202	0.318	266	0.226	4985	X-RAY DIFFRACTION	99.9619
2.202-2.275	0.321	271	0.23	4795	X-RAY DIFFRACTION	99.9605
2.275-2.354	0.305	242	0.205	4643	X-RAY DIFFRACTION	100
2.354-2.443	0.278	226	0.189	4534	X-RAY DIFFRACTION	100
2.443-2.543	0.27	214	0.192	4351	X-RAY DIFFRACTION	100
2.543-2.656	0.278	213	0.177	4178	X-RAY DIFFRACTION	99.9772
2.656-2.786	0.27	205	0.176	3974	X-RAY DIFFRACTION	100
2.786-2.936	0.29	193	0.186	3812	X-RAY DIFFRACTION	100
2.936-3.114	0.272	189	0.16	3615	X-RAY DIFFRACTION	99.9737
3.114-3.329	0.285	173	0.177	3406	X-RAY DIFFRACTION	100
3.329-3.596	0.263	176	0.182	3147	X-RAY DIFFRACTION	100
3.596-3.939	0.278	151	0.157	2955	X-RAY DIFFRACTION	100
3.939-4.403	0.217	103	0.144	2681	X-RAY DIFFRACTION	100
4.403-5.083	0.233	140	0.151	2359	X-RAY DIFFRACTION	100
5.083-6.223	0.218	105	0.137	2029	X-RAY DIFFRACTION	100
6.223-8.789	0.297	77	0.174	1601	X-RAY DIFFRACTION	100

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