PDB-9viu: Crystal structure of WCK4234 in complex with SME-1

ID or keywords:

Entry

Database: PDB / ID: 9viu

Title

Crystal structure of WCK4234 in complex with SME-1

Components

Beta-lactamase SME-1

Keywords

HYDROLASE / DBO / acyl enzyme complex / covalent adduct

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: 2.8 Å

Authors

Dhankhar, K. / Hazra, S.

Funding support

India, 2items

Citation

Journal: To Be Published
Title: Crystal structure of WCK4234 in complex with SME-1
Authors: Dhankhar, K. / Hazra, S.

History

Deposition	Jun 18, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 24, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9viu.cif.gz	256.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9viu.ent.gz	152 KB	Display	PDB format
PDBx/mmJSON format	9viu.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/vi/9viu ftp://data.pdbj.org/pub/pdb/validation_reports/vi/9viu	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

61.4 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&software
Evidence: gel filtration
30.7 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&software
30.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	35.374, 51.484, 129.687
Angle α, β, γ (deg.)	90, 90.72, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 267 / Label seq-ID: 3 - 269

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#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-C8Y / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carbonitrile / open form - WCK 4234 Mass: 249.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₇H₁₁N₃O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.94 Å³/Da / Density % sol: 36.66 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M lithium chloride, PEG 4000 20%

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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: Dec 17, 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: 2.8→29.15 Å / Num. obs: 11713 / % possible obs: 99.8 % / Redundancy: 7.7 % / CC_1/2: 0.987 / R_pim(I) all: 0.112 / Net I/σ(I): 7.4
Reflection shell	Resolution: 2.8→2.95 Å / Num. unique obs: 1729 / CC_1/2: 0.929

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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: 2.8→21.622 Å / Cor.coef. F_o:F_c: 0.901 / Cor.coef. F_o:F_c free: 0.829 / SU B: 44.378 / SU ML: 0.399 / Cross valid method: FREE R-VALUE / ESU R Free: 0.529

	R_factor	Num. reflection	% reflection
R_free	0.3031	538	4.601 %
R_work	0.2363	11156	-
all	0.239	-	-
obs	-	11694	99.625 %

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: 4.964 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.597 Å²	0 Å²	0.05 Å²
2-	-	-1.155 Å²	-0 Å²
3-	-	-	1.75 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→21.622 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4116	0	34	48	4198

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	4220
X-RAY DIFFRACTION	r_angle_refined_deg	1.53	1.819	5690
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.563	5	532
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.61	5	32
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.97	10	742
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.457	10	186
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	626
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3182
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	2020
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	2927
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.221	0.2	164
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.303	0.2	83
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.31	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	34.96	0.438	2134
X-RAY DIFFRACTION	r_mcangle_it	44.135	0.732	2664
X-RAY DIFFRACTION	r_scbond_it	0.778	0.385	2086
X-RAY DIFFRACTION	r_scangle_it	1.533	0.705	3026
X-RAY DIFFRACTION	r_lrange_it	49.19	4.522	6525
X-RAY DIFFRACTION	r_rigid_bond_restr	5.873	3	4220
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.048	0.05	8952

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.04845	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.04845	0.0501

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
2.8-2.872	0.342	53	0.286	801	0.29	854	0.91	0.951	100	0.263
2.872-2.949	0.382	41	0.272	800	0.277	841	0.914	0.952	100	0.254
2.949-3.033	0.341	41	0.238	744	0.243	785	0.9	0.965	100	0.222
3.033-3.124	0.328	32	0.24	754	0.244	786	0.922	0.965	100	0.218
3.124-3.224	0.318	26	0.225	734	0.228	761	0.948	0.968	99.8686	0.207
3.224-3.335	0.333	21	0.209	683	0.213	705	0.946	0.971	99.8582	0.191
3.335-3.458	0.254	27	0.226	703	0.227	730	0.954	0.968	100	0.206
3.458-3.595	0.294	39	0.227	636	0.231	676	0.941	0.968	99.8521	0.214
3.595-3.75	0.362	27	0.245	619	0.25	646	0.918	0.966	100	0.23
3.75-3.927	0.317	36	0.233	626	0.237	662	0.948	0.97	100	0.219
3.927-4.132	0.258	15	0.213	547	0.214	564	0.973	0.974	99.6454	0.203
4.132-4.373	0.206	37	0.236	559	0.234	598	0.97	0.97	99.6656	0.226
4.373-4.661	0.309	18	0.237	496	0.24	517	0.963	0.967	99.4197	0.231
4.661-5.015	0.342	27	0.239	488	0.245	515	0.938	0.967	100	0.227
5.015-5.464	0.21	20	0.234	439	0.233	459	0.955	0.97	100	0.225
5.464-6.061	0.451	23	0.255	407	0.264	430	0.921	0.966	100	0.241
6.061-6.909	0.423	12	0.261	373	0.266	385	0.904	0.965	100	0.244
6.909-8.254	0.168	18	0.219	307	0.216	325	0.969	0.977	100	0.214
8.254-10.905	0.181	17	0.169	260	0.17	277	0.975	0.982	100	0.162
10.905-21.622	0.299	8	0.273	180	0.274	191	0.979	0.968	98.4293	0.278

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