PDB-9ujc: Crystal Structure of SME-1 E166A with cefpirome

ID or keywords:

Entry

Database: PDB / ID: 9ujc

Title

Crystal Structure of SME-1 E166A with cefpirome

Components

Beta-lactamase SME-1

Keywords

HYDROLASE / Acyl Enzyme Complex / Carbapenemase

Function / homology

Function and homology information

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

Biological species

Serratia marcescens (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Dhankhar, K. / Hazra, S.

Funding support

India, 2items

Citation

Journal: To Be Published
Title: Crystal Structure of SME-1 E166A with cefpirome
Authors: Dhankhar, K. / Hazra, S.

History

Deposition	Apr 17, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 22, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ujc.cif.gz	261.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9ujc.ent.gz	170.8 KB	Display	PDB format
PDBx/mmJSON format	9ujc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uj/9ujc ftp://data.pdbj.org/pub/pdb/validation_reports/uj/9ujc	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 (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2) #29 - May 2002 Penicillin-binding Proteins similarity (1)

Deposited unit

A: Beta-lactamase SME-1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	36.516, 49.888, 61.153
Angle α, β, γ (deg.)	90, 99.298, 90
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase SME-1 Mass: 30345.266 Da / Num. of mol.: 1 / Mutation: E166A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) Gene: SME-1, blaSME-1, blaSME-4, blaSME1, bpl-1, bplA, sme-2, smeA Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52682, beta-lactamase
#2: Chemical	ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form Mass: 397.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₁₅N₅O₅S₂ Details: The reported chirality issue at atom C6 of residue CEF (chain A, residue 301) is expected and arises from the covalent acyl-enzyme complex formation between Ser70 of the enzyme and the C8 ...Details: The reported chirality issue at atom C6 of residue CEF (chain A, residue 301) is expected and arises from the covalent acyl-enzyme complex formation between Ser70 of the enzyme and the C8 atom of the ligand. This covalent linkage results in opening of the beta-lactam ring and a consequent rearrangement of the ligand geometry within the active site. Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.81 Å³/Da / Density % sol: 31.97 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, 0.2M lithium chloride

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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: Mar 5, 2024
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→25.82 Å / Num. obs: 14812 / % possible obs: 99.9 % / Redundancy: 7.8 % / CC_1/2: 0.997 / Net I/σ(I): 13.2
Reflection shell	Resolution: 2→2.05 Å / Num. unique obs: 6569 / CC_1/2: 0.921

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
CrysalisPro		data reduction
CrysalisPro		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→25.82 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.928 / SU B: 10.613 / SU ML: 0.129 / Cross valid method: FREE R-VALUE / ESU R Free: 0.177

	R_factor	Num. reflection	% reflection
R_free	0.2195	739	4.995 %
R_work	0.1558	14055	-
all	0.159	-	-
obs	-	14794	99.838 %

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: 17.842 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.763 Å²	0 Å²	-2.586 Å²
2-	-	-0.352 Å²	0 Å²
3-	-	-	1.862 Å²

Refinement step

Cycle: LAST / Resolution: 2→25.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2054	0	38	98	2190

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	2135
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2028
X-RAY DIFFRACTION	r_angle_refined_deg	1.917	1.825	2879
X-RAY DIFFRACTION	r_angle_other_deg	0.625	1.791	4667
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.69	5	268
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	17.19	7.5	24
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	5.42	17	5
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.676	10	370
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.191	10	92
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	315
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2556
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	492
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	481
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	1893
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1079
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	1196
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.241	0.2	111
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.269	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.226	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.268	0.2	47
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.141	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	3.235	1.573	1072
X-RAY DIFFRACTION	r_mcbond_other	3.181	1.573	1072
X-RAY DIFFRACTION	r_mcangle_it	5.115	2.821	1340
X-RAY DIFFRACTION	r_mcangle_other	5.121	2.824	1341
X-RAY DIFFRACTION	r_scbond_it	4.862	1.875	1063
X-RAY DIFFRACTION	r_scbond_other	4.844	1.872	1060
X-RAY DIFFRACTION	r_scangle_it	7.461	3.317	1539
X-RAY DIFFRACTION	r_scangle_other	7.441	3.312	1534
X-RAY DIFFRACTION	r_lrange_it	24.447	18.169	2508
X-RAY DIFFRACTION	r_lrange_other	24.325	17.847	2492
X-RAY DIFFRACTION	r_rigid_bond_restr	3.644	3	4163

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 (%)
2-2.052	0.263	48	0.17	1031	X-RAY DIFFRACTION	99.7227
2.052-2.108	0.24	54	0.168	989	X-RAY DIFFRACTION	100
2.108-2.168	0.209	46	0.161	996	X-RAY DIFFRACTION	100
2.168-2.234	0.229	51	0.171	921	X-RAY DIFFRACTION	100
2.234-2.307	0.244	47	0.149	942	X-RAY DIFFRACTION	100
2.307-2.387	0.21	56	0.157	876	X-RAY DIFFRACTION	100
2.387-2.477	0.23	45	0.139	852	X-RAY DIFFRACTION	100
2.477-2.577	0.243	55	0.142	819	X-RAY DIFFRACTION	100
2.577-2.69	0.254	38	0.142	792	X-RAY DIFFRACTION	100
2.69-2.82	0.193	34	0.158	779	X-RAY DIFFRACTION	100
2.82-2.971	0.239	33	0.168	720	X-RAY DIFFRACTION	100
2.971-3.148	0.237	43	0.162	695	X-RAY DIFFRACTION	100
3.148-3.362	0.269	35	0.165	632	X-RAY DIFFRACTION	100
3.362-3.626	0.24	41	0.166	607	X-RAY DIFFRACTION	99.3865
3.626-3.965	0.131	18	0.15	556	X-RAY DIFFRACTION	99.6528
3.965-4.42	0.239	26	0.128	511	X-RAY DIFFRACTION	99.4444
4.42-5.079	0.173	24	0.141	458	X-RAY DIFFRACTION	100
5.079-6.161	0.181	19	0.183	384	X-RAY DIFFRACTION	100
6.161-8.475	0.151	16	0.16	302	X-RAY DIFFRACTION	100
8.475-25.82	0.163	10	0.171	193	X-RAY DIFFRACTION	98.0676

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