PDB-9uj6: Crystal structure of SME-1 E166A in complex with cefsulodin

ID or keywords:

Entry

Database: PDB / ID: 9uj6

Title

Crystal structure of SME-1 E166A in complex with cefsulodin

Components

Beta-lactamase SME-1

Keywords

HYDROLASE / Carbapenemase / deacylation deficient mutant / complex

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 in complex with cefsulodin
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	9uj6.cif.gz	271.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9uj6.ent.gz	176.3 KB	Display	PDB format
PDBx/mmJSON format	9uj6.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/9uj6 ftp://data.pdbj.org/pub/pdb/validation_reports/uj/9uj6	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

B: Beta-lactamase SME-1

hetero molecules

61.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-lactamase SME-1

hetero molecules

defined by author
Evidence: gel filtration
30.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Beta-lactamase SME-1

hetero molecules

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

Unit cell

Length a, b, c (Å)	36.268, 51.046, 131.316
Angle α, β, γ (deg.)	90, 92.78, 90
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase SME-1 Mass: 30403.297 Da / Num. of mol.: 2 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-3LU / 1-({(2R)-4-carboxy-2-[(R)-carboxy{[(2R)-2-phenyl-2-sulfoacetyl]amino}methyl]-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium / Cefsulodin, bound form Mass: 508.545 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₂N₃O₈S₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 189 / 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 Å³/Da / Density % sol: 38.4 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M lithium chloride, 20% PEG4000

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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: Apr 10, 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→23.33 Å / Num. obs: 32693 / % possible obs: 99.9 % / Redundancy: 4.9 % / CC_1/2: 0.989 / Net I/σ(I): 9.7
Reflection shell	Resolution: 2→2.05 Å / Num. unique obs: 2380 / CC_1/2: 0.624

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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→22.403 Å / Cor.coef. F_o:F_c: 0.918 / Cor.coef. F_o:F_c free: 0.867 / SU B: 13.709 / SU ML: 0.162 / Cross valid method: FREE R-VALUE / ESU R Free: 0.204

	R_factor	Num. reflection	% reflection
R_free	0.268	1636	5.006 %
R_work	0.2001	31044	-
all	0.204	-	-
obs	-	32680	99.869 %

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: 15.001 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.615 Å²	0 Å²	-0.431 Å²
2-	-	-2.462 Å²	-0 Å²
3-	-	-	3.105 Å²

Refinement step

Cycle: LAST / Resolution: 2→22.403 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4108	0	54	189	4351

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	4236
X-RAY DIFFRACTION	r_angle_refined_deg	2.07	1.825	5716
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.409	5	532
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	15.805	6.667	36
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.498	10	738
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.207	10	184
X-RAY DIFFRACTION	r_chiral_restr	0.139	0.2	628
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3212
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	2013
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	2918
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.2	0.2	244
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.26	0.2	53
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.204	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	2.799	1.38	2134
X-RAY DIFFRACTION	r_mcangle_it	4.54	2.48	2664
X-RAY DIFFRACTION	r_scbond_it	3.516	1.499	2102
X-RAY DIFFRACTION	r_scangle_it	5.388	2.701	3052
X-RAY DIFFRACTION	r_lrange_it	11.789	15.89	6590
X-RAY DIFFRACTION	r_rigid_bond_restr	3.411	3	4236

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
2-2.052	0.392	131	0.275	2229	0.281	2366	0.911	0.953	99.7464	0.269
2.052-2.107	0.286	137	0.219	2211	0.222	2348	0.944	0.972	100	0.207
2.107-2.168	0.337	110	0.245	2167	0.25	2277	0.92	0.961	100	0.235
2.168-2.234	0.307	107	0.208	2069	0.213	2176	0.939	0.973	100	0.194
2.234-2.306	0.333	85	0.216	2039	0.221	2124	0.924	0.97	100	0.202
2.306-2.386	0.287	98	0.206	1962	0.21	2060	0.951	0.973	100	0.191
2.386-2.475	0.304	89	0.22	1892	0.224	1981	0.941	0.968	100	0.205
2.475-2.575	0.235	84	0.194	1862	0.196	1946	0.963	0.976	100	0.178
2.575-2.688	0.267	94	0.189	1745	0.193	1839	0.945	0.977	100	0.174
2.688-2.817	0.252	106	0.178	1663	0.183	1769	0.962	0.981	100	0.166
2.817-2.967	0.31	93	0.216	1582	0.221	1675	0.933	0.969	100	0.199
2.967-3.144	0.316	94	0.206	1495	0.212	1590	0.936	0.973	99.9371	0.194
3.144-3.356	0.248	86	0.213	1430	0.215	1517	0.963	0.973	99.9341	0.204
3.356-3.618	0.246	75	0.211	1339	0.212	1415	0.964	0.977	99.9293	0.205
3.618-3.953	0.196	45	0.171	1237	0.172	1286	0.98	0.984	99.689	0.165
3.953-4.403	0.202	66	0.155	1115	0.157	1181	0.979	0.986	100	0.15
4.403-5.051	0.183	33	0.149	1018	0.15	1051	0.985	0.989	100	0.144
5.051-6.109	0.247	37	0.185	877	0.188	914	0.975	0.984	100	0.175
6.109-8.336	0.169	30	0.179	682	0.178	712	0.978	0.989	100	0.171
8.336-22.403	0.218	36	0.179	429	0.182	467	0.987	0.989	99.5717	0.174

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