PDB-5ypn: Crystal structure of NDM-1 bound to hydrolyzed meropenem represen...

ID or keywords:

Entry

Database: PDB / ID: 5ypn

Title

Crystal structure of NDM-1 bound to hydrolyzed meropenem representing an EI2 complex

Components

Metallo-beta-lactamase NDM-1

Keywords

HYDROLASE / MDM-1 / meropenem / EI2 complex

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.12 Å

Authors

Feng, H. / Liu, W. / Wang, D.

Citation

Journal: Nat Commun / Year: 2017
Title: The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis.
Authors: Feng, H. / Liu, X. / Wang, S. / Fleming, J. / Wang, D.C. / Liu, W.

History

Deposition	Nov 2, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ypn.cif.gz	190.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5ypn.ent.gz	152 KB	Display	PDB format
PDBx/mmJSON format	5ypn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ypn_validation.pdf.gz	995.2 KB	Display	wwPDB validaton report
Full document	5ypn_full_validation.pdf.gz	1001.5 KB	Display
Data in XML	5ypn_validation.xml.gz	21.5 KB	Display
Data in CIF	5ypn_validation.cif.gz	29.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yp/5ypn ftp://data.pdbj.org/pub/pdb/validation_reports/yp/5ypn	HTTPS FTP

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Related structure data

Related structure data	5ypiC 5ypkC 5yplC 5ypmC 4rl0S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5zgx-d 6ibs-2 6c6i-1 6xbe-4 5ypl-2 5ypm-2 6lj5-d 5ypk-6 5ypi-4 6ny7-d 5ypl-1 5ypm-5 6d1g-d 6mgy-2 5ypk-8 6q30-1 5ypi-1 5zgf-d 4rm5-3 4tze-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#187 - Jul 2015
New Delhi Metallo-β-Lactamase
similarity (3)
#105 - Sep 2008
Ribonuclease A
similarity (2)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#22 - Oct 2001
Photosystem I
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#29 - May 2002
Penicillin-binding Proteins
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Metallo-beta-lactamase NDM-1

B: Metallo-beta-lactamase NDM-1

hetero molecules

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

1

A: Metallo-beta-lactamase NDM-1

hetero molecules

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

2

B: Metallo-beta-lactamase NDM-1

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.730, 73.510, 76.530
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Metallo-beta-lactamase NDM-1 Mass: 25631.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A7Y424, UniProt: E5KIY2*PLUS
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-LMP / (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoy l)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid / Hydrolyzed Meropenem Mass: 401.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₇N₃O₆S
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.89 Å³/Da / Density % sol: 34.77 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 28% (w/v) PEG 3350, 0.1M Bis-Tris, pH 5.8, 0.2M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97772 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97772 Å / Relative weight: 1
Reflection	Resolution: 2.12→41.98 Å / Num. obs: 42452 / % possible obs: 99.8 % / Redundancy: 3.85 % / R_sym value: 0.109 / Net I/σ(I): 10.66
Reflection shell	Resolution: 2.12→2.18 Å / Redundancy: 3.52 % / Mean I/σ(I) obs: 2.18 / R_sym value: 0.621 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4RL0

4rl0

Resolution: 2.12→41.978 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 23.68 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS

	R_factor	Num. reflection	% reflection
R_free	0.2439	3717	8.77 %
R_work	0.2039	-	-
obs	0.2074	42401	99.76 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.12→41.978 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3394	0	68	176	3638

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.028	3561
X-RAY DIFFRACTION	f_angle_d	0.995	4826
X-RAY DIFFRACTION	f_dihedral_angle_d	11.444	2140
X-RAY DIFFRACTION	f_chiral_restr	0.064	542
X-RAY DIFFRACTION	f_plane_restr	0.006	634

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 (%)
2.12-2.1468	0.3082	132	0.2931	1457	X-RAY DIFFRACTION	100
2.1468-2.1751	0.3225	135	0.2861	1412	X-RAY DIFFRACTION	100
2.1751-2.2049	0.3143	139	0.2735	1447	X-RAY DIFFRACTION	100
2.2049-2.2364	0.2595	153	0.2627	1430	X-RAY DIFFRACTION	100
2.2364-2.2698	0.305	128	0.2576	1425	X-RAY DIFFRACTION	100
2.2698-2.3052	0.2984	155	0.2621	1415	X-RAY DIFFRACTION	100
2.3052-2.343	0.3078	132	0.25	1473	X-RAY DIFFRACTION	100
2.343-2.3834	0.301	129	0.239	1425	X-RAY DIFFRACTION	100
2.3834-2.4267	0.2506	136	0.2339	1414	X-RAY DIFFRACTION	100
2.4267-2.4734	0.3187	138	0.2403	1459	X-RAY DIFFRACTION	100
2.4734-2.5239	0.2529	127	0.2182	1442	X-RAY DIFFRACTION	100
2.5239-2.5788	0.2466	141	0.2296	1434	X-RAY DIFFRACTION	100
2.5788-2.6387	0.2711	150	0.225	1433	X-RAY DIFFRACTION	100
2.6387-2.7047	0.2505	112	0.2104	1432	X-RAY DIFFRACTION	100
2.7047-2.7778	0.2349	153	0.213	1404	X-RAY DIFFRACTION	100
2.7778-2.8596	0.2828	146	0.2096	1467	X-RAY DIFFRACTION	100
2.8596-2.9518	0.3078	132	0.2054	1439	X-RAY DIFFRACTION	100
2.9518-3.0573	0.2485	140	0.2071	1413	X-RAY DIFFRACTION	100
3.0573-3.1797	0.1991	133	0.1965	1419	X-RAY DIFFRACTION	100
3.1797-3.3243	0.2073	156	0.1862	1449	X-RAY DIFFRACTION	100
3.3243-3.4995	0.2443	131	0.1841	1405	X-RAY DIFFRACTION	100
3.4995-3.7187	0.2036	132	0.1797	1427	X-RAY DIFFRACTION	99
3.7187-4.0056	0.2097	144	0.1774	1420	X-RAY DIFFRACTION	99
4.0056-4.4083	0.1944	140	0.1644	1426	X-RAY DIFFRACTION	100
4.4083-5.0452	0.2368	148	0.1628	1433	X-RAY DIFFRACTION	99
5.0452-6.3529	0.2529	127	0.1951	1440	X-RAY DIFFRACTION	100
6.3529-41.9861	0.2097	128	0.1927	1444	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.0571	-0.9119	-0.7868	3.919	0.4479	1.7548	0.0387	-0.384	-0.2078	0.2963	0.0585	-0.0259	0.4132	-0.1336	-0.0384	0.3784	-0.0214	-0.0215	0.2568	0.0439	0.2599	-53.5534	59.7731	98.3918
2	1.7217	-0.6359	0.5714	4.8443	0.0452	2.2696	-0.0957	-0.1204	0.0373	0.0307	0.0808	-0.3365	0.2093	0.2164	-0.0605	0.2546	0.0051	-0.0289	0.2297	-0.0002	0.1443	-48.1599	66.6214	95.5137
3	1.31	-0.2534	0.0358	4.0739	-0.0212	0.9921	-0.0319	-0.0838	-0.263	-0.206	-0.0024	0.1549	0.3499	-0.046	-0.0583	0.2907	-0.0577	-0.0105	0.2424	-0.0331	0.1696	-56.8874	64.055	88.6817
4	0.6224	-0.4165	0.1565	3.9449	0.0091	0.8518	-0.1496	0.0313	-0.0169	-0.5905	0.145	-0.1211	0.1278	-0.1433	-0.0377	0.3359	-0.0445	0.0451	0.2237	0.0047	0.1499	-52.7228	78.2885	84.114
5	1.2787	-0.177	-0.251	4.3506	-0.1879	1.121	-0.0493	-0.0644	0.0623	-0.0467	0.0729	0.2308	0.0292	-0.2748	-0.0494	0.22	-0.0197	-0.0214	0.2624	0.0085	0.115	-57.9606	80.7296	95.8744
6	0.5874	-0.3372	0.2215	4.1482	0.019	0.9399	-0.0993	-0.0635	-0.0288	0.4151	0.201	-0.4036	-0.1125	0.1548	-0.0189	0.2092	0.0151	-0.0127	0.3103	-0.0139	0.1788	-48.902	81.4582	103.2434
7	2.0079	-0.0686	0.2391	3.9291	0.3022	1.6982	0.0177	-0.2231	0.1422	0.6451	0.0508	-0.5722	-0.1872	0.3105	-0.0594	0.436	0.0088	-0.0831	0.2709	-0.0326	0.2179	-45.6554	85.8353	108.3855
8	0.9884	-1.1172	-0.2476	1.8597	1.0195	2.8955	-0.011	0.1791	0.3621	-1.0593	-0.1407	-0.7327	-0.3351	0.4403	-0.1476	0.6505	-0.0512	0.1901	0.3028	0.0495	0.4871	-49.4721	121.8891	78.5928
9	1.6311	0.3789	0.7314	2.9461	0.1005	1.3803	-0.0044	-0.1173	0.0725	-0.1415	-0.0947	-0.7698	-0.0717	0.2455	-0.0632	0.2919	-0.119	0.1293	0.2528	-0.0443	0.5645	-43.9232	116.2304	87.5238
10	1.3149	-0.2723	-0.0003	4.2609	0.0846	1.3412	-0.0251	-0.0968	0.409	-0.3082	0.0681	-0.056	-0.1732	-0.0879	-0.0049	0.2688	-0.0116	0.0032	0.217	-0.0257	0.2972	-55.8412	114.3887	85.3135
11	1.2715	-0.3852	-0.2686	3.3749	-0.1631	1.3884	0.0959	0.0723	0.1025	-0.6289	0.013	-0.2103	-0.1668	-0.0152	-0.0098	0.3342	-0.014	0.0495	0.2077	-0.0493	0.2192	-54.3311	100.0798	82.9512
12	0.5597	-0.0123	-0.0169	1.0877	0.2111	1.0123	0.0444	-0.0659	0.3419	-0.1858	0.0102	-1.1766	-0.1691	0.2744	-0.0114	0.2811	0.0223	-0.0064	0.315	-0.078	0.9691	-36.3014	98.5226	86.3172
13	0.2722	-0.0867	0.0445	0.3652	0.3235	0.3632	0.0217	0.2644	0.1739	-0.4869	0.0153	-0.3193	-0.1606	0.0351	-0.0545	0.7137	-0.1256	0.7652	0.2739	0.1054	0.8282	-43.224	102.358	74.7434
14	1.3047	-0.2802	0.0104	0.73	-0.3509	0.4099	0.0934	0.0291	0.0378	-0.2786	-0.0106	-0.5789	-0.0278	0.2344	0.312	0.6034	0.047	0.6197	0.4621	0.0257	1.1159	-34.2646	96.6759	77.8552

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 43 through 57 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 82 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 83 through 118 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 119 through 166 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 167 through 212 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 213 through 255 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 256 through 270 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 43 through 57 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 58 through 70 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 71 through 137 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 138 through 212 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 213 through 228 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 229 through 255 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 256 through 270 )

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