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

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Basic information

Entry
Database: PDB / ID: 6rmf
TitleCrystal structure of NDM-1 with VNRX-5133
ComponentsMetallo-beta-lactamase type 2
KeywordsANTIMICROBIAL 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
Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-K9B / Chem-K9K / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsHinchliffe, P. / Spencer, J. / Brem, J. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: 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
DepositionMay 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: 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 2.0Oct 30, 2019Group: 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 3.0May 13, 2020Group: 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 3.1Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,28412
Polymers51,5522
Non-polymers1,73310
Water7,620423
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9898
Polymers25,7761
Non-polymers1,2147
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2954
Polymers25,7761
Non-polymers5193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number19
Space group name H-MP212121

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Components

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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

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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 / Sulfate


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 / Water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.56 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.51→52.34 Å / Num. obs: 64647 / % possible obs: 100 % / Redundancy: 11.9 % / CC1/2: 0.99 / Rpim(I) all: 0.103 / Net I/σ(I): 8
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3144 / CC1/2: 0.421 / Rpim(I) all: 1.304 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 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
RfactorNum. reflection% reflection
Rfree0.1724 3421 5.3 %
Rwork0.1456 --
obs0.147 64525 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.51→42.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 92 423 3949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093645
X-RAY DIFFRACTIONf_angle_d0.9484977
X-RAY DIFFRACTIONf_dihedral_angle_d17.1391261
X-RAY DIFFRACTIONf_chiral_restr0.06551
X-RAY DIFFRACTIONf_plane_restr0.007648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.53160.25361390.22062484X-RAY DIFFRACTION100
1.5316-1.55450.2161680.21032483X-RAY DIFFRACTION100
1.5545-1.57870.23911560.2032493X-RAY DIFFRACTION100
1.5787-1.60460.23051490.19192521X-RAY DIFFRACTION100
1.6046-1.63230.2141240.19322520X-RAY DIFFRACTION100
1.6323-1.6620.21121570.18022489X-RAY DIFFRACTION100
1.662-1.69390.18471530.1772520X-RAY DIFFRACTION100
1.6939-1.72850.20181610.16812501X-RAY DIFFRACTION100
1.7285-1.76610.191400.15692527X-RAY DIFFRACTION100
1.7661-1.80720.17631720.14462499X-RAY DIFFRACTION100
1.8072-1.85240.16871330.14692525X-RAY DIFFRACTION100
1.8524-1.90250.18091360.14062540X-RAY DIFFRACTION100
1.9025-1.95850.15951310.13042538X-RAY DIFFRACTION100
1.9585-2.02170.15731300.12862567X-RAY DIFFRACTION100
2.0217-2.09390.14821420.13192516X-RAY DIFFRACTION100
2.0939-2.17780.18341540.12972532X-RAY DIFFRACTION100
2.1778-2.27690.18721240.12462575X-RAY DIFFRACTION100
2.2769-2.39690.141210.12842551X-RAY DIFFRACTION100
2.3969-2.5470.1469980.12742617X-RAY DIFFRACTION100
2.547-2.74370.13751380.13212576X-RAY DIFFRACTION100
2.7437-3.01970.15281710.13952540X-RAY DIFFRACTION100
3.0197-3.45650.17561630.13342569X-RAY DIFFRACTION100
3.4565-4.35420.14631520.12382622X-RAY DIFFRACTION100
4.3542-42.71470.18071090.16392799X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.19960.6875-0.34113.5136-0.19022.82410.0409-0.4058-0.14820.31080.0253-0.45020.2060.42630.01060.15420.018-0.03720.15360.02920.142319.2781-12.815523.1377
22.80550.1430.06682.47530.23022.8291-0.0440.0075-0.07260.02610.0102-0.10090.0950.0744-0.02270.04520.00920.00860.0250.01070.069816.2086-8.682214.7441
30.3063-0.2481-0.21852.15630.18160.8829-0.0070.03120.0126-0.14510.0036-0.0234-0.01380.01040.00110.0467-0.0052-0.00770.06630.01010.064913.66813.68078.4185
44.08431.1772.09342.23680.68951.8633-0.02220.07060.12790.0024-0.02350.0829-0.0734-0.07890.04410.05010.00450.00360.05860.00550.053510.65789.066615.747
56.64631.84071.58682.7290.77533.34720.088-0.2697-0.06220.1538-0.04540.01170.0359-0.0338-0.06090.06620.0207-0.0030.05660.01730.056715.23672.685525.6982
66.1269-2.43660.89967.6422-1.43884.9469-0.11840.1220.3028-0.0649-0.1139-0.6511-0.32570.47440.01020.089-0.0459-0.03310.17940.01390.162128.519512.469421.3674
71.5263-0.44950.43384.70930.13182.4844-0.0563-0.0973-0.06810.25560.05410.0905-0.0262-0.02930.01870.05480.0029-0.01130.09270.00980.040916.14295.682227.6645
86.23784.3447-3.15738.8522-2.39667.4323-0.0669-0.18390.10040.1537-0.0057-0.4188-0.40930.37140.04630.1069-0.0014-0.04330.09190.0110.094823.981112.151831.3584
91.5069-0.29550.07923.71592.58654.7243-0.01770.24330.3604-0.39850.1922-0.2209-0.52340.4258-0.13670.1797-0.02540.05570.10530.02470.175819.113549.3650.6521
105.2232-0.00652.55683.1976-0.17216.72860.0288-0.27010.24070.2995-0.0299-0.4828-0.06860.51410.05950.109-0.0059-0.01260.0993-0.02350.194623.947842.88318.4726
112.4747-0.07710.88673.09170.054.23530.0550.04120.0158-0.033-0.01640.03130.0379-0.0406-0.06220.0628-0.00690.02050.02730.00230.101814.670640.07975.1277
124.7913-1.59331.76515.92-1.5626.3368-0.1816-0.09630.23730.16250.09280.0473-0.3248-0.16770.05550.08270.00110.02570.0619-0.02540.148211.694548.43929.2175
130.5410.199-0.16841.96630.10451.02210.0234-0.03380.080.2236-0.01560.1991-0.0349-0.0530.00320.0724-0.00170.0270.07550.00160.126411.125330.765911.3353
144.89110.17490.6881.91030.20912.60120.0520.05450.0308-0.0163-0.02420.12940.0186-0.1424-0.03680.0613-0.010.01170.04120.00420.082413.223925.21033.9304
154.6582-1.35680.84682.1099-0.84283.71590.0860.14410.1057-0.20150.0071-0.07150.0378-0.0786-0.09550.0826-0.00620.03910.0393-0.00580.075122.204532.1816-1.8949
162.31710.54840.19312.7867-0.25712.72670.0074-0.0241-0.01780.00470.0067-0.1917-0.02310.1221-0.02520.0232-0.00180.03650.0804-0.01120.104326.639727.73191.276
178.0015-1.75264.23153.7982-1.51157.1260.0196-0.1545-0.18390.05360.0293-0.20690.12820.1613-0.04940.0701-0.01210.04920.0897-0.00650.145233.525823.9018-0.9122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 108 )
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 170 )
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 194 )
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 215 )
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 228 )
7X-RAY DIFFRACTION7chain 'A' and (resid 229 through 255 )
8X-RAY DIFFRACTION8chain 'A' and (resid 256 through 270 )
9X-RAY DIFFRACTION9chain 'B' and (resid 40 through 57 )
10X-RAY DIFFRACTION10chain 'B' and (resid 58 through 67 )
11X-RAY DIFFRACTION11chain 'B' and (resid 71 through 94 )
12X-RAY DIFFRACTION12chain 'B' and (resid 95 through 108 )
13X-RAY DIFFRACTION13chain 'B' and (resid 109 through 170 )
14X-RAY DIFFRACTION14chain 'B' and (resid 171 through 194 )
15X-RAY DIFFRACTION15chain 'B' and (resid 195 through 215 )
16X-RAY DIFFRACTION16chain 'B' and (resid 216 through 255 )
17X-RAY DIFFRACTION17chain 'B' and (resid 256 through 270 )

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