PDB-6rmf: Crystal structure of NDM-1 with VNRX-5133

ID or keywords:

Entry

Database: PDB / ID: 6rmf

Title

Crystal structure of NDM-1 with VNRX-5133

Components

Metallo-beta-lactamase type 2

Keywords

ANTIMICROBIAL PROTEIN / metallo-beta-lactamase / antibiotic resistance / inhibitor

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.51 Å

Authors

Hinchliffe, P. / Spencer, J. / Brem, J. / Schofield, C.J.

Funding support

United Kingdom, 1items

Citation

Journal: J.Med.Chem. / Year: 2019
Title: Bicyclic Boronate VNRX-5133 Inhibits Metallo- and Serine-beta-Lactamases.
Authors: Krajnc, A. / Brem, J. / Hinchliffe, P. / Calvopina, K. / Panduwawala, T.D. / Lang, P.A. / Kamps, J.J.A.G. / Tyrrell, J.M. / Widlake, E. / Saward, B.G. / Walsh, T.R. / Spencer, J. / Schofield, C.J.

History

Deposition	May 6, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 11, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 2.0	Oct 30, 2019	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary Category: chem_comp / entity / pdbx_entity_nonpoly Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 3.0	May 13, 2020	Group: Derived calculations / Non-polymer description / Structure summary Category: chem_comp / entity / pdbx_entity_nonpoly Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 3.1	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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	6rmf.cif.gz	275.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6rmf.ent.gz	223.9 KB	Display	PDB format
PDBx/mmJSON format	6rmf.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6rmf_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	6rmf_full_validation.pdf.gz	1.5 MB	Display
Data in XML	6rmf_validation.xml.gz	24 KB	Display
Data in CIF	6rmf_validation.cif.gz	35.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rm/6rmf ftp://data.pdbj.org/pub/pdb/validation_reports/rm/6rmf	HTTPS FTP

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Related structure data

Related structure data	6rtnC 3spuS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ypk-3 5ypm-5 5ypi-4 6ibv-2 5ypm-1 6xbf-3 5ypn-2 6d1j-d 5ypi-1 5ypm-4 5ypm-2 5ypl-2 5ypn-1 6c6i-1 5ypi-2 4rm5-2 6mgy-2 6tbr-2 6ibs-2 6zyq-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

6rtnC

3spuS

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 (4) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Metallo-beta-lactamase type 2

B: Metallo-beta-lactamase type 2

hetero molecules

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

1

A: Metallo-beta-lactamase type 2

hetero molecules

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

2

B: Metallo-beta-lactamase type 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.821, 73.837, 77.681
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1 Mass: 25775.951 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7C422, beta-lactamase

#1: Protein

Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...

Mass: 25775.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7C422, beta-lactamase

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Non-polymers , 5 types, 433 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-K9K / (10aR)-2-(((1r,4R)-4-((2-aminoethyl)amino)cyclohexyl)methyl)-6-carboxy-4-hydroxy-4,10a-dihydro-10H-benzo[5,6][1,2]oxaborinino[2,3-b][1,4,2]oxazaborol-4-uide Mass: 388.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₉H₂₇BN₃O₅ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-K9B / (4~{R})-4-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid Mass: 406.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₂₉BN₃O₆ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 423 / 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: 1.97 Å³/Da / Density % sol: 37.56 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1M bis-tris pH 5.8, 32% PEG 3350, 0.15M NH4SO4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96863 Å / Relative weight: 1
Reflection	Resolution: 1.51→52.34 Å / Num. obs: 64647 / % possible obs: 100 % / Redundancy: 11.9 % / CC_1/2: 0.99 / R_pim(I) all: 0.103 / Net I/σ(I): 8
Reflection shell	Resolution: 1.51→1.54 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3144 / CC_1/2: 0.421 / R_pim(I) all: 1.304 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.15.2_3472: ???)	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3SPU

3spu

Resolution: 1.51→42.698 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.26

	R_factor	Num. reflection	% reflection
R_free	0.1724	3421	5.3 %
R_work	0.1456	-	-
obs	0.147	64525	99.96 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.51→42.698 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3434	0	92	423	3949

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3645
X-RAY DIFFRACTION	f_angle_d	0.948	4977
X-RAY DIFFRACTION	f_dihedral_angle_d	17.139	1261
X-RAY DIFFRACTION	f_chiral_restr	0.06	551
X-RAY DIFFRACTION	f_plane_restr	0.007	648

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 (%)
1.51-1.5316	0.2536	139	0.2206	2484	X-RAY DIFFRACTION	100
1.5316-1.5545	0.216	168	0.2103	2483	X-RAY DIFFRACTION	100
1.5545-1.5787	0.2391	156	0.203	2493	X-RAY DIFFRACTION	100
1.5787-1.6046	0.2305	149	0.1919	2521	X-RAY DIFFRACTION	100
1.6046-1.6323	0.214	124	0.1932	2520	X-RAY DIFFRACTION	100
1.6323-1.662	0.2112	157	0.1802	2489	X-RAY DIFFRACTION	100
1.662-1.6939	0.1847	153	0.177	2520	X-RAY DIFFRACTION	100
1.6939-1.7285	0.2018	161	0.1681	2501	X-RAY DIFFRACTION	100
1.7285-1.7661	0.19	140	0.1569	2527	X-RAY DIFFRACTION	100
1.7661-1.8072	0.1763	172	0.1446	2499	X-RAY DIFFRACTION	100
1.8072-1.8524	0.1687	133	0.1469	2525	X-RAY DIFFRACTION	100
1.8524-1.9025	0.1809	136	0.1406	2540	X-RAY DIFFRACTION	100
1.9025-1.9585	0.1595	131	0.1304	2538	X-RAY DIFFRACTION	100
1.9585-2.0217	0.1573	130	0.1286	2567	X-RAY DIFFRACTION	100
2.0217-2.0939	0.1482	142	0.1319	2516	X-RAY DIFFRACTION	100
2.0939-2.1778	0.1834	154	0.1297	2532	X-RAY DIFFRACTION	100
2.1778-2.2769	0.1872	124	0.1246	2575	X-RAY DIFFRACTION	100
2.2769-2.3969	0.14	121	0.1284	2551	X-RAY DIFFRACTION	100
2.3969-2.547	0.1469	98	0.1274	2617	X-RAY DIFFRACTION	100
2.547-2.7437	0.1375	138	0.1321	2576	X-RAY DIFFRACTION	100
2.7437-3.0197	0.1528	171	0.1395	2540	X-RAY DIFFRACTION	100
3.0197-3.4565	0.1756	163	0.1334	2569	X-RAY DIFFRACTION	100
3.4565-4.3542	0.1463	152	0.1238	2622	X-RAY DIFFRACTION	100
4.3542-42.7147	0.1807	109	0.1639	2799	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	3.1996	0.6875	-0.3411	3.5136	-0.1902	2.8241	0.0409	-0.4058	-0.1482	0.3108	0.0253	-0.4502	0.206	0.4263	0.0106	0.1542	0.018	-0.0372	0.1536	0.0292	0.1423	19.2781	-12.8155	23.1377
2	2.8055	0.143	0.0668	2.4753	0.2302	2.8291	-0.044	0.0075	-0.0726	0.0261	0.0102	-0.1009	0.095	0.0744	-0.0227	0.0452	0.0092	0.0086	0.025	0.0107	0.0698	16.2086	-8.6822	14.7441
3	0.3063	-0.2481	-0.2185	2.1563	0.1816	0.8829	-0.007	0.0312	0.0126	-0.1451	0.0036	-0.0234	-0.0138	0.0104	0.0011	0.0467	-0.0052	-0.0077	0.0663	0.0101	0.0649	13.6681	3.6807	8.4185
4	4.0843	1.177	2.0934	2.2368	0.6895	1.8633	-0.0222	0.0706	0.1279	0.0024	-0.0235	0.0829	-0.0734	-0.0789	0.0441	0.0501	0.0045	0.0036	0.0586	0.0055	0.0535	10.6578	9.0666	15.747
5	6.6463	1.8407	1.5868	2.729	0.7753	3.3472	0.088	-0.2697	-0.0622	0.1538	-0.0454	0.0117	0.0359	-0.0338	-0.0609	0.0662	0.0207	-0.003	0.0566	0.0173	0.0567	15.2367	2.6855	25.6982
6	6.1269	-2.4366	0.8996	7.6422	-1.4388	4.9469	-0.1184	0.122	0.3028	-0.0649	-0.1139	-0.6511	-0.3257	0.4744	0.0102	0.089	-0.0459	-0.0331	0.1794	0.0139	0.1621	28.5195	12.4694	21.3674
7	1.5263	-0.4495	0.4338	4.7093	0.1318	2.4844	-0.0563	-0.0973	-0.0681	0.2556	0.0541	0.0905	-0.0262	-0.0293	0.0187	0.0548	0.0029	-0.0113	0.0927	0.0098	0.0409	16.1429	5.6822	27.6645
8	6.2378	4.3447	-3.1573	8.8522	-2.3966	7.4323	-0.0669	-0.1839	0.1004	0.1537	-0.0057	-0.4188	-0.4093	0.3714	0.0463	0.1069	-0.0014	-0.0433	0.0919	0.011	0.0948	23.9811	12.1518	31.3584
9	1.5069	-0.2955	0.0792	3.7159	2.5865	4.7243	-0.0177	0.2433	0.3604	-0.3985	0.1922	-0.2209	-0.5234	0.4258	-0.1367	0.1797	-0.0254	0.0557	0.1053	0.0247	0.1758	19.1135	49.365	0.6521
10	5.2232	-0.0065	2.5568	3.1976	-0.1721	6.7286	0.0288	-0.2701	0.2407	0.2995	-0.0299	-0.4828	-0.0686	0.5141	0.0595	0.109	-0.0059	-0.0126	0.0993	-0.0235	0.1946	23.9478	42.8831	8.4726
11	2.4747	-0.0771	0.8867	3.0917	0.05	4.2353	0.055	0.0412	0.0158	-0.033	-0.0164	0.0313	0.0379	-0.0406	-0.0622	0.0628	-0.0069	0.0205	0.0273	0.0023	0.1018	14.6706	40.0797	5.1277
12	4.7913	-1.5933	1.7651	5.92	-1.562	6.3368	-0.1816	-0.0963	0.2373	0.1625	0.0928	0.0473	-0.3248	-0.1677	0.0555	0.0827	0.0011	0.0257	0.0619	-0.0254	0.1482	11.6945	48.4392	9.2175
13	0.541	0.199	-0.1684	1.9663	0.1045	1.0221	0.0234	-0.0338	0.08	0.2236	-0.0156	0.1991	-0.0349	-0.053	0.0032	0.0724	-0.0017	0.027	0.0755	0.0016	0.1264	11.1253	30.7659	11.3353
14	4.8911	0.1749	0.688	1.9103	0.2091	2.6012	0.052	0.0545	0.0308	-0.0163	-0.0242	0.1294	0.0186	-0.1424	-0.0368	0.0613	-0.01	0.0117	0.0412	0.0042	0.0824	13.2239	25.2103	3.9304
15	4.6582	-1.3568	0.8468	2.1099	-0.8428	3.7159	0.086	0.1441	0.1057	-0.2015	0.0071	-0.0715	0.0378	-0.0786	-0.0955	0.0826	-0.0062	0.0391	0.0393	-0.0058	0.0751	22.2045	32.1816	-1.8949
16	2.3171	0.5484	0.1931	2.7867	-0.2571	2.7267	0.0074	-0.0241	-0.0178	0.0047	0.0067	-0.1917	-0.0231	0.1221	-0.0252	0.0232	-0.0018	0.0365	0.0804	-0.0112	0.1043	26.6397	27.7319	1.276
17	8.0015	-1.7526	4.2315	3.7982	-1.5115	7.126	0.0196	-0.1545	-0.1839	0.0536	0.0293	-0.2069	0.1282	0.1613	-0.0494	0.0701	-0.0121	0.0492	0.0897	-0.0065	0.1452	33.5258	23.9018	-0.9122

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 33 through 57 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 108 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 109 through 170 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 171 through 194 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 195 through 215 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 216 through 228 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 229 through 255 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 256 through 270 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 40 through 57 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 58 through 67 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 71 through 94 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 95 through 108 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 109 through 170 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 171 through 194 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 195 through 215 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 216 through 255 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 256 through 270 )

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Protein , 1 types, 2 molecules AB

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-Yorodumi

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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

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Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 433 molecules

-
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

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Yorodumi