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- PDB-5n4s: VIM-2 metallo-beta-lactamase in complex with ((S)-3-mercapto-2-me... -

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Basic information

Entry
Database: PDB / ID: 5n4s
TitleVIM-2 metallo-beta-lactamase in complex with ((S)-3-mercapto-2-methylpropanoyl)-D-tryptophan (Compound 3)
ComponentsBeta-lactamase VIM-2
KeywordsHYDROLASE / metallo-beta-lactamase / inhibitor / complex / antibiotic resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal 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
FORMIC ACID / Chem-R38 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsLi, G.-B. / Brem, J. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Chem. Commun. (Camb.) / Year: 2017
Title: Crystallographic analyses of isoquinoline complexes reveal a new mode of metallo-beta-lactamase inhibition.
Authors: Li, G.B. / Brem, J. / Lesniak, R. / Abboud, M.I. / Lohans, C.T. / Clifton, I.J. / Yang, S.Y. / Jimenez-Castellanos, J.C. / Avison, M.B. / Spencer, J. / McDonough, M.A. / Schofield, C.J.
History
DepositionFeb 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_CC_half
Revision 1.3Jan 17, 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 / diffrn_radiation_wavelength / 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 / _diffrn_radiation_wavelength.wavelength / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase VIM-2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,66616
Polymers49,3852
Non-polymers1,28114
Water9,224512
1
A: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2877
Polymers24,6921
Non-polymers5956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3799
Polymers24,6921
Non-polymers6878
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.845, 80.308, 68.732
Angle α, β, γ (deg.)90.000, 130.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-849-

HOH

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Components

#1: Protein Beta-lactamase VIM-2 / Class B beta-lactamase / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta- ...Class B beta-lactamase / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-2 / Metallo-beta-lactamase vim-2 / VIM-2 metallo-beta-lactamase / VIM-2 protein


Mass: 24692.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255
Plasmid: opinf vector based / Details (production host): plasmid derived / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q9K2N0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-R38 / (2~{R})-3-(1~{H}-indol-3-yl)-2-[[(2~{S})-2-methyl-3-sulfanyl-propanoyl]amino]propanoic acid


Mass: 306.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H18N2O3S
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M Magnesium Formate, 21%~27% (v/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→52.21 Å / Num. obs: 132440 / % possible obs: 98.89 % / Redundancy: 6.6 % / Biso Wilson estimate: 10.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.026
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.387 / Mean I/σ(I) obs: 1.3 / Num. unique all: 6825 / % possible all: 97.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.01 Å52.21 Å
Translation5.01 Å52.21 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1c1d

1c1d


Resolution: 1.2→52.213 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.25
RfactorNum. reflection% reflection
Rfree0.2002 6391 4.86 %
Rwork0.184 --
obs0.1848 131443 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.56 Å2 / Biso mean: 18.3805 Å2 / Biso min: 6.53 Å2
Refinement stepCycle: final / Resolution: 1.2→52.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3419 0 69 518 4006
Biso mean--24.03 30.43 -
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0223681
X-RAY DIFFRACTIONf_angle_d1.025005
X-RAY DIFFRACTIONf_chiral_restr0.084568
X-RAY DIFFRACTIONf_plane_restr0.007663
X-RAY DIFFRACTIONf_dihedral_angle_d17.0051260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.21360.37711900.37854043423395
1.2136-1.22790.38122300.38363981421195
1.2279-1.24290.42462120.37254067427995
1.2429-1.25860.38832020.37194013421595
1.2586-1.27520.39362280.36524030425896
1.2752-1.29270.36952020.35854051425396
1.2927-1.31110.33742060.33614088429496
1.3111-1.33070.34972040.33074100430497
1.3307-1.35150.32142470.31974084433197
1.3515-1.37370.33912430.31284117436097
1.3737-1.39730.33481950.30034126432197
1.3973-1.42280.32051920.28234169436198
1.4228-1.45010.29712020.27884168437098
1.4501-1.47970.27352220.25844171439398
1.4797-1.51190.26281940.24524164435898
1.5119-1.54710.23132000.2354233443399
1.5471-1.58580.22732240.21854167439199
1.5858-1.62860.23422010.19884225442699
1.6286-1.67660.22691780.18714267444599
1.6766-1.73070.19052030.169142544457100
1.7307-1.79250.16921920.15574228442099
1.7925-1.86430.17532260.149641884414100
1.8643-1.94920.16342320.142542274459100
1.9492-2.05190.15732140.139942564470100
2.0519-2.18050.15242080.133342624470100
2.1805-2.34890.15942090.133142744483100
2.3489-2.58520.15332190.130642524471100
2.5852-2.95930.15172410.135642504491100
2.9593-3.72820.15332810.134242114492100
3.7282-52.26260.14691940.141543864580100
Refinement TLS params.

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

IDL11 (°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)
10.81861.8655-1.19118.89240.1093.5012-0.1460.48130.81470.6760.00330.9456-0.5125-0.7932-0.02740.19130.0934-0.06740.32560.04360.3948-35.65250.723751.0021
23.3389-0.1230.20683.5535-0.00933.2068-0.06160.12320.2417-0.0586-0.05230.2595-0.138-0.29720.06940.0536-0.0028-0.02440.1294-0.01090.1068-27.5059-5.973448.1872
32.47450.4863-1.35953.7055-1.06886.00950.02520.08380.0462-0.30560.04460.47250.0314-0.4604-0.04360.0759-0.0155-0.01890.2118-0.05820.1956-35.211-11.186546.0752
42.04220.45920.36772.36351.28371.92330.00450.0015-0.1660.1923-0.06220.09990.2361-0.1260.00530.0893-0.02740.01860.0808-0.01170.0915-22.9287-16.564854.3135
51.07630.17390.25751.98190.45991.26160.01350.0902-0.07650.04010.015-0.09450.06750.0363-0.02320.0560.0020.00110.0882-0.00360.0738-13.2323-10.830651.9882
62.4708-2.11581.62554.8902-2.83354.4804-0.035-0.27050.10240.3810.0890.1583-0.1901-0.2965-0.05180.1212-0.01960.0020.1232-0.01590.118-18.97193.842961.758
74.7602-0.2794-1.6352.66722.03928.19140.02750.03110.11520.01290.071-0.2559-0.12210.4538-0.08220.0548-0.0136-0.01810.06990.01150.1036-6.0319-0.060556.8905
85.6681-0.0303-3.05881.55860.02634.37230.01690.25660.2382-0.2299-0.0369-0.0242-0.2312-0.0633-0.00720.1044-0.0109-0.00930.08870.02210.0737-16.76042.367647.0491
94.39690.38392.49094.32712.80377.01930.0468-0.12720.11050.07280.0394-0.0740.07470.0788-0.07640.0572-0.0019-0.0040.06430.00140.1181-11.8878.234960.8956
105.64052.0253-3.84059.3732-1.35628.0678-0.11470.9137-0.7212-0.99780.4372-0.21840.9307-0.219-0.31610.3268-0.0123-0.08910.3236-0.08380.2443-44.02188.353461.0673
113.4564-0.31970.07943.81860.01123.59070.07260.215-0.1915-0.0873-0.0160.1420.2262-0.07360.00890.07450.0133-0.01790.10150.00280.0723-46.49615.248769.9022
128.35321.91140.99553.7741-0.75034.8925-0.07110.34870.0048-0.24740.10980.28450.0607-0.1687-0.03180.11810.038-0.02210.13530.00830.0881-48.885921.02262.47
134.4849-0.59241.38211.3189-0.69442.4310.06820.12750.0212-0.0136-0.03590.0637-0.0903-0.0545-0.03270.08250.01130.00710.05520.00850.0582-41.459822.057572.9764
141.4254-0.25970.07871.7453-0.74632.4430.018-0.02630.12360.20770.0019-0.0353-0.24380.0737-0.01670.1328-0.00020.00230.0661-0.00460.0692-36.940927.747178.5685
151.1533-0.01560.38731.6308-0.32021.3992-0.0101-0.0265-0.06450.1550.03070.0298-0.03-0.027-0.01950.0746-0.0030.0080.07590.01260.0663-39.338912.219581.6892
167.4295-0.8937-1.87742.2222-0.04254.3527-0.0978-0.4161-0.1810.31750.04920.02210.05190.04130.0710.1177-0.002-0.01140.07550.02970.0727-35.45568.189490.1424
173.12-0.1185-2.13491.22650.29746.18660.00230.0875-0.14170.07740.04070.24330.1906-0.3771-0.01230.0626-0.00690.01220.07930.01580.1112-46.13656.224280.1083
185.5496-1.96011.06281.97120.07652.6591-0.0052-0.0110.00680.11610.0229-0.07890.14060.1195-0.01950.1202-0.0013-0.01350.07360.01520.1016-32.27140.41383.3879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 32 through 44 )B32 - 44
2X-RAY DIFFRACTION2chain 'B' and (resid 45 through 88 )B45 - 88
3X-RAY DIFFRACTION3chain 'B' and (resid 89 through 102 )B89 - 102
4X-RAY DIFFRACTION4chain 'B' and (resid 103 through 145 )B103 - 145
5X-RAY DIFFRACTION5chain 'B' and (resid 146 through 199 )B146 - 199
6X-RAY DIFFRACTION6chain 'B' and (resid 200 through 215 )B200 - 215
7X-RAY DIFFRACTION7chain 'B' and (resid 216 through 229 )B216 - 229
8X-RAY DIFFRACTION8chain 'B' and (resid 230 through 245 )B230 - 245
9X-RAY DIFFRACTION9chain 'B' and (resid 246 through 262 )B246 - 262
10X-RAY DIFFRACTION10chain 'A' and (resid 32 through 44 )A32 - 44
11X-RAY DIFFRACTION11chain 'A' and (resid 45 through 88 )A45 - 88
12X-RAY DIFFRACTION12chain 'A' and (resid 89 through 102 )A89 - 102
13X-RAY DIFFRACTION13chain 'A' and (resid 103 through 122 )A103 - 122
14X-RAY DIFFRACTION14chain 'A' and (resid 123 through 163 )A123 - 163
15X-RAY DIFFRACTION15chain 'A' and (resid 164 through 215 )A164 - 215
16X-RAY DIFFRACTION16chain 'A' and (resid 216 through 229 )A216 - 229
17X-RAY DIFFRACTION17chain 'A' and (resid 230 through 245 )A230 - 245
18X-RAY DIFFRACTION18chain 'A' and (resid 246 through 262 )A246 - 262

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