PDB-8xy8: a beta-lactamase - AmpC

Basic information

• Entry: Database: PDB / ID: 8xy8
• Title: a beta-lactamase - AmpC
• Components: Beta-lactamase
• Keywords: HYDROLASE / beta-lactamase

Function / homology

Function:

antibiotic catabolic process / beta-lactamase / beta-lactamase activity / outer membrane-bounded periplasmic space / response to antibiotic

Domain/homology:

Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like

Component:

Beta-lactamase

• Biological species: Paraburkholderia xenovorans (bacteria)
• Method: X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
• Authors: Ma, W.Z. / Song, W.

Funding support

1items

Organization	Grant number	Country
Not funded

• Citation: Journal: To Be Published; Title: Mechanism-Guided Protein Engineering of Paraburkholderia xenovorans Lactamase for the Green Synthesis of 2-(2-oxopyrrolidin-1-yl)-butanoic acid; Authors: Ma, W.Z. / Song, W.

History

Deposition	Jan 19, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 22, 2025	Provider: repository / Type: Initial release

Assembly

Deposited unit

A: Beta-lactamase

Summary:

• 41.8 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	41,831	1
Polymers	41,831	1
Non-polymers	0	0
Water	829	46

1

Summary:

• Idetical with deposited unit
• defined by author

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Unit cell

Length a, b, c (Å)	84.940, 84.940, 120.600
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P41212

Components

#1: Protein

A Beta-lactamase / PxAmpC

Details:

Mass: 41831.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia xenovorans (bacteria) / Gene: Bxe_B1593 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13NG8, beta-lactamase

#2: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H₂O

• Has protein modification: Y

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.6 ų/Da / Density % sol: 52.69 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, sitting drop; Details: 1 M sodium phosphate (pH 7.5), 0.7 M ammonium sulfate

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
• Detector: Type: Bruker PHOTON II / Detector: PIXEL / Date: Sep 8, 2022
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.54178 Å / Relative weight: 1
• Reflection: Resolution: 2.39→42.59 Å / Num. obs: 18029 / % possible obs: 99.9 % / Redundancy: 8.9 % / R_merge(I) obs: 0.151 / Net I/σ(I): 11.9
• Reflection shell: Resolution: 2.39→2.49 Å / R_merge(I) obs: 0.885 / Num. unique obs: 1823

Processing

• Software: Name: REFMAC / Version: 5.8.0267 / Classification: refinement

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→42.59 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.909 / SU B: 9.564 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.25465	895	5 %	RANDOM
Rwork	0.21139	-	-	-
obs	0.21361	17082	99.78 %	-

• 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: 28.591 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-1.51 Å2	-0 Å2	-0 Å2
2-	-	-1.51 Å2	-0 Å2
3-	-	-	3.02 Å2

Refinement step

Cycle: 1 / Resolution: 2.39→42.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2715	0	0	46	2761

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	2775
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	2677
X-RAY DIFFRACTION	r_angle_refined_deg	1.425	1.647	3773
X-RAY DIFFRACTION	r_angle_other_deg	1.197	1.575	6169
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.126	5	359
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.693	23.051	118
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.092	15	454
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.597	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	371
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3157
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	603
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	1.625	2.915	1439
X-RAY DIFFRACTION	r_mcbond_other	1.622	2.911	1437
X-RAY DIFFRACTION	r_mcangle_it	2.618	4.369	1797
X-RAY DIFFRACTION	r_mcangle_other	2.619	4.368	1797
X-RAY DIFFRACTION	r_scbond_it	1.942	3.153	1336
X-RAY DIFFRACTION	r_scbond_other	1.941	3.155	1337
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.273	4.617	1977
X-RAY DIFFRACTION	r_long_range_B_refined	4.546	33.967	3001
X-RAY DIFFRACTION	r_long_range_B_other	4.538	33.992	2997
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.395→2.457 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.444	53	-
Rwork	0.357	1227	-
obs	-	-	98.23 %