PDB-8j6y: Crystal structure of class A beta-lactamase PSE-4 WT- Apo state

ID or keywords:

Entry

Database: PDB / ID: 8j6y

Title

Crystal structure of class A beta-lactamase PSE-4 WT- Apo state

Components

Beta-lactamase PSE-4

Keywords

HYDROLASE / Antimicrobial resistance / Beta-lactamase / pseudomonas aeruginosa / carbenicillinase

Function / homology

Function and homology information

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

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Sarkar, M. / Bhattacharya, S. / Hazra, S.

Funding support

India, 3items

Organization	Grant number	Country
Indian Council of Medical Research	5/3/8/17/GIA-ITR	India
Indian Council of Medical Research	BIC/12(15)/2014	India
Science and Engineering Research Board (SERB)	YSS/2014/000492	India

Citation

Journal: To be published
Title: Crystal structure of class A beta-lactamase PSE-4 WT- Apo state
Authors: Sarkar, M. / Bhattacharya, S. / Hazra, S.

History

Deposition	Apr 26, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 1, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 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	8j6y.cif.gz	116.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8j6y_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	8j6y_full_validation.pdf.gz	2.5 MB	Display
Data in XML	8j6y_validation.xml.gz	12.4 KB	Display
Data in CIF	8j6y_validation.cif.gz	16.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j6/8j6y ftp://data.pdbj.org/pub/pdb/validation_reports/j6/8j6y	HTTPS FTP

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Related structure data

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	#164 - Aug 2013 Serotonin Receptor similarity (5) #29 - May 2002 Penicillin-binding Proteins similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2)

Deposited unit

A: Beta-lactamase PSE-4

hetero molecules

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

1

A: Beta-lactamase PSE-4

hetero molecules

A: Beta-lactamase PSE-4

hetero molecules

defined by author&software
Evidence: gel filtration
64.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.951, 95.951, 61.509
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Beta-lactamase PSE-4 / Beta-lactamase CARB-1 / Carbenicillinase 1 Mass: 31435.541 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pse4, carB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16897, beta-lactamase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.25 Å³/Da / Density % sol: 45.46 % / Description: single crystal with diamond like shape
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.5 M Ammonium sulfate, 0.1 M BIS-TRIS propane pH 7.0 PH range: 5.8 - 7.2

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å

Detector

Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 16, 2023 / Details: X ray Optics

Radiation

Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.54 Å / Relative weight: 1

Reflection

Resolution: 2.4→27.226 Å / Num. obs: 11708 / % possible obs: 98.9 % / Redundancy: 19.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.153 / R_pim(I) all: 0.049 / R_rim(I) all: 0.161 / Net I/σ(I): 14.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
8.98-27.21	11.4	0.03	266	1	0.011	0.032
2.4-2.49	19.4	1.228	1182	0.955	0.4	1.292

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
CrysalisPro		data collection
Coot		model building
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→27.226 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.888 / SU B: 11.473 / SU ML: 0.255 / Cross valid method: FREE R-VALUE / ESU R: 0.486 / ESU R Free: 0.331
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2719	573	4.954 %
R_work	0.2088	10993	-
all	0.213	-	-
obs	-	11566	77.9944 %

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: 42.031 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.611 Å²	0 Å²	0 Å²
2-	-	-2.611 Å²	0 Å²
3-	-	-	5.223 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→27.226 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2038	0	40	75	2153

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	2102
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1982
X-RAY DIFFRACTION	r_angle_refined_deg	1.559	1.633	2856
X-RAY DIFFRACTION	r_angle_other_deg	0.502	1.568	4560
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.335	5	265
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.925	5	10
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.207	10	359
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.918	10	91
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	336
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2434
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	462
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	451
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.199	0.2	1872
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	1072
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	1129
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.199	0.2	81
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.07	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.214	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.17	0.2	72
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.126	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	4.033	4.136	1063
X-RAY DIFFRACTION	r_mcbond_other	4.016	4.137	1063
X-RAY DIFFRACTION	r_mcangle_it	5.628	7.411	1327
X-RAY DIFFRACTION	r_mcangle_other	5.626	7.415	1328
X-RAY DIFFRACTION	r_scbond_it	4.703	4.657	1039
X-RAY DIFFRACTION	r_scbond_other	4.149	4.529	1008
X-RAY DIFFRACTION	r_scangle_it	6.786	8.354	1529
X-RAY DIFFRACTION	r_scangle_other	6.235	8.139	1482
X-RAY DIFFRACTION	r_lrange_it	9.139	38.616	2386
X-RAY DIFFRACTION	r_lrange_other	9.07	38.508	2377

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.4-2.462	0.434	53	0.282	769	0.292	828	0.892	0.944	99.2754	0.257
2.462-2.529	0.329	40	0.282	770	0.284	819	0.939	0.949	98.9011	0.25
2.529-2.602	0.358	49	0.263	750	0.269	806	0.902	0.952	99.1315	0.232
2.602-2.681	0.38	37	0.254	706	0.26	752	0.902	0.955	98.8032	0.219
2.681-2.768	0.34	36	0.269	714	0.273	762	0.938	0.955	98.4252	0.23
2.768-2.864	0.371	36	0.267	685	0.273	732	0.901	0.952	98.4973	0.226
2.864-2.971	0.408	28	0.265	656	0.271	697	0.92	0.951	98.1349	0.223
2.971-3.091	0.369	36	0.259	654	0.265	695	0.919	0.956	99.2806	0.217
3.091-3.226	0.322	35	0.239	601	0.243	646	0.926	0.963	98.452	0.208
3.226-3.381	0.242	26	0.237	595	0.237	632	0.95	0.966	98.2595	0.205
3.381-3.561	0.382	31	0.22	564	0.227	605	0.889	0.971	98.3471	0.192
3.561-3.773	0.283	29	0.214	539	0.218	569	0.935	0.974	99.8243	0.187
3.773-4.028	0.261	28	0.19	501	0.193	541	0.958	0.978	97.7819	0.171
4.028-4.343	0.325	17	0.156	486	0.161	503	0.957	0.983	100	0.136
4.343-4.746	0.282	21	0.15	458	0.155	480	0.958	0.986	99.7917	0.132
4.746-5.286	0.206	16	0.144	405	0.146	421	0.981	0.988	100	0.133
5.286-6.066	0.267	24	0.189	369	0.194	393	0.964	0.981	100	0.168
6.066-7.338	0.182	13	0.173	323	0.174	336	0.972	0.98	100	0.162
7.338-10.02	0.166	13	0.154	265	0.155	278	0.985	0.985	100	0.155
10.02-27.226	0.387	5	0.199	183	0.205	189	0.769	0.968	99.4709	0.193

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