PDB-9il8: Crystal Structure of SME-1 Class A Carbapenemase in complex with ...

ID or keywords:

Entry

Database: PDB / ID: 9il8

Title

Crystal Structure of SME-1 Class A Carbapenemase in complex with Durlobactam

Components

beta-lactamase

Keywords

HYDROLASE / Acyl Enzyme Complex / Carbapenemase / DBO

Function / homology

Function and homology information

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

Biological species

Serratia marcescens (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Dhankhar, K. / Hazra, S.

Funding support

India, 2items

Citation

Journal: To Be Published
Title: Crystal Structure of SME-1 Class A Carbapenemase in complex with Durlobactam
Authors: Dhankhar, K. / Hazra, S.

History

Deposition	Jun 29, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 2, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9il8.cif.gz	269.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9il8.ent.gz	174.8 KB	Display	PDB format
PDBx/mmJSON format	9il8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9il8_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	9il8_full_validation.pdf.gz	1.8 MB	Display
Data in XML	9il8_validation.xml.gz	26.5 KB	Display
Data in CIF	9il8_validation.cif.gz	35.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/il/9il8 ftp://data.pdbj.org/pub/pdb/validation_reports/il/9il8	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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

B: beta-lactamase

hetero molecules

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

1

A: beta-lactamase

hetero molecules

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

2

B: beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	35.355, 50.746, 129.9
Angle α, β, γ (deg.)	90, 92.705, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
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-2, blaSME-1, blaSME-4, blaSME1, SME12620_22 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54488, beta-lactamase
#2: Chemical	ChemComp-JXG / (2S,5R)-1-formyl-3-methyl-5-[(sulfooxy)amino]-1,2,5,6-tetrahydropyridine-2-carboxamide / ETX2514 bound form Mass: 279.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₃N₃O₆S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.98 Å³/Da / Density % sol: 37.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 3350, 0.2M Lithium Chloride

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
Detector	Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 29, 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: 2.3→25.95 Å / Num. obs: 20681 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC_1/2: 0.994 / R_rim(I) all: 0.166 / Net I/σ(I): 7.5
Reflection shell	Resolution: 2.3→2.38 Å / Num. unique obs: 15588 / CC_1/2: 0.938

-
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: 2.3→25.386 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.885 / SU B: 20.972 / SU ML: 0.224 / Cross valid method: FREE R-VALUE / ESU R Free: 0.293

	R_factor	Num. reflection	% reflection
R_free	0.2682	1028	4.974 %
R_work	0.1926	19638	-
all	0.196	-	-
obs	-	20666	99.802 %

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: 14.082 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.603 Å²	-0 Å²	-0.517 Å²
2-	-	-1.689 Å²	0 Å²
3-	-	-	-0.862 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→25.386 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4120	0	51	115	4286

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	4240
X-RAY DIFFRACTION	r_angle_refined_deg	2.397	1.821	5712
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.038	5	532
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.235	5	34
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.598	10	746
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.25	10	186
X-RAY DIFFRACTION	r_chiral_restr	0.149	0.2	626
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3198
X-RAY DIFFRACTION	r_nbd_refined	0.23	0.2	2053
X-RAY DIFFRACTION	r_nbtor_refined	0.313	0.2	2932
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.227	0.2	215
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.344	0.2	72
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.177	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	3.731	1.248	2134
X-RAY DIFFRACTION	r_mcangle_it	5.886	2.243	2664
X-RAY DIFFRACTION	r_scbond_it	4.974	1.389	2106
X-RAY DIFFRACTION	r_scangle_it	7.351	2.483	3048
X-RAY DIFFRACTION	r_lrange_it	29.462	15.127	6628
X-RAY DIFFRACTION	r_rigid_bond_restr	5.476	3	4240
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.099	0.05	8808

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	0.09858	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09858	0.05008

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
2.3-2.359	0.328	71	0.244	1442	0.248	1513	0.915	0.96	100	0.224
2.359-2.423	0.309	79	0.229	1366	0.233	1445	0.936	0.967	100	0.211
2.423-2.493	0.295	67	0.192	1374	0.197	1441	0.928	0.977	100	0.173
2.493-2.569	0.269	83	0.187	1311	0.193	1394	0.953	0.978	100	0.168
2.569-2.652	0.311	67	0.2	1255	0.205	1322	0.941	0.975	100	0.178
2.652-2.744	0.313	59	0.21	1269	0.215	1328	0.937	0.973	100	0.188
2.744-2.847	0.307	79	0.187	1169	0.194	1248	0.952	0.978	100	0.167
2.847-2.961	0.295	53	0.196	1189	0.2	1242	0.948	0.976	100	0.173
2.961-3.091	0.227	46	0.163	1105	0.166	1151	0.968	0.984	100	0.147
3.091-3.239	0.252	40	0.174	1095	0.177	1135	0.951	0.981	100	0.157
3.239-3.412	0.219	71	0.19	965	0.193	1037	0.974	0.979	99.9036	0.173
3.412-3.614	0.277	41	0.182	974	0.186	1017	0.951	0.982	99.8033	0.171
3.614-3.858	0.238	41	0.208	911	0.21	952	0.972	0.973	100	0.199
3.858-4.16	0.308	43	0.178	840	0.184	888	0.953	0.982	99.4369	0.171
4.16-4.544	0.242	46	0.189	777	0.192	824	0.962	0.974	99.8786	0.181
4.544-5.061	0.215	50	0.162	707	0.166	759	0.971	0.986	99.7365	0.157
5.061-5.805	0.24	27	0.171	634	0.174	661	0.979	0.983	100	0.161
5.805-7.019	0.256	29	0.2	548	0.203	577	0.977	0.978	100	0.19
7.019-9.567	0.271	19	0.174	434	0.178	454	0.971	0.983	99.7797	0.173
9.567-25.386	0.204	17	0.219	273	0.218	298	0.982	0.978	97.3154	0.221

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi