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- PDB-6ew3: Crystal structure of the metallo-beta-lactamase VIM-2 with ML302F -

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Basic information

Entry
Database: PDB / ID: 6ew3
TitleCrystal structure of the metallo-beta-lactamase VIM-2 with ML302F
ComponentsMetallo-beta-lactamase VIM-2
KeywordsHYDROLASE / metal binding / ANTIBIOTIC RESISTANCE / xchem / complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Chem-S3C / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsCollins, P.M. / Brem, J. / McDonough, M.A. / van Berkel, S.S. / von Delft, F. / Schofield, C.J.
CitationJournal: Bioorg. Med. Chem. / Year: 2018
Title: Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-beta-lactamases.
Authors: Zhang, D. / Markoulides, M.S. / Stepanovs, D. / Rydzik, A.M. / El-Hussein, A. / Bon, C. / Kamps, J.J.A.G. / Umland, K.D. / Collins, P.M. / Cahill, S.T. / Wang, D.Y. / von Delft, F. / Brem, J. ...Authors: Zhang, D. / Markoulides, M.S. / Stepanovs, D. / Rydzik, A.M. / El-Hussein, A. / Bon, C. / Kamps, J.J.A.G. / Umland, K.D. / Collins, P.M. / Cahill, S.T. / Wang, D.Y. / von Delft, F. / Brem, J. / McDonough, M.A. / Schofield, C.J.
History
DepositionNov 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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 / 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_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.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: Metallo-beta-lactamase VIM-2
B: Metallo-beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,02519
Polymers49,5332
Non-polymers1,49217
Water4,612256
1
A: Metallo-beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4959
Polymers24,7671
Non-polymers7288
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,53010
Polymers24,7671
Non-polymers7649
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.480, 78.910, 67.460
Angle α, β, γ (deg.)90.000, 130.480, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-696-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallo-beta-lactamase VIM-2


Mass: 24766.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM-2 / Production host: Escherichia coli (E. coli) / References: UniProt: D1MEN9

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Non-polymers , 6 types, 273 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-S3C / (2Z)-2-sulfanyl-3-(2,3,6-trichlorophenyl)prop-2-enoic acid


Mass: 283.559 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H5Cl3O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1mM TCEP, 10mM ML302, 50mM HEPES pH 7.5, 100mM NaCl, 0.1mM ZnCl2, 0.1M magnesium formate, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.14→51.32 Å / Num. obs: 22190 / % possible obs: 98.2 % / Redundancy: 3.4 % / CC1/2: 0.982 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.106 / Rrim(I) all: 0.154 / Net I/σ(I): 8.7
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1632 / CC1/2: 0.699 / Rpim(I) all: 0.479 / Rrim(I) all: 0.707 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.22data extraction
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ3

4bz3


Resolution: 2.14→51.312 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.99
RfactorNum. reflection% reflection
Rfree0.2096 1107 4.99 %
Rwork0.1691 --
obs0.1711 22188 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.79 Å2 / Biso mean: 26.9173 Å2 / Biso min: 8.29 Å2
Refinement stepCycle: final / Resolution: 2.14→51.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 65 256 3803
Biso mean--32.69 32.04 -
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023763
X-RAY DIFFRACTIONf_angle_d0.5415165
X-RAY DIFFRACTIONf_chiral_restr0.046579
X-RAY DIFFRACTIONf_plane_restr0.003709
X-RAY DIFFRACTIONf_dihedral_angle_d11.0982200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.14-2.23740.27921660.22462604277098
2.2374-2.35540.27511380.20772475261393
2.3554-2.5030.23271400.18552649278998
2.503-2.69620.20821320.170226782810100
2.6962-2.96750.19651210.16626862807100
2.9675-3.39680.21791270.15492675280299
3.3968-4.27930.18171540.14172610276498
4.2793-51.3270.18531290.17172704283398
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)
10.38830.3109-0.16511.37561.10571.57310.0972-0.5328-0.23560.44620.5561-0.20420.29750.66390.21640.36490.094-0.03540.32940.12710.3025-14.28650.350367.6086
20.49590.18150.15140.50150.13290.22460.2126-0.2421-0.18990.2798-0.0245-0.21180.02880.07320.02690.18970.0115-0.02750.17820.01690.2838-12.80474.723861.7956
30.2753-0.07560.32550.1720.05910.56910.06370.01590.04060.1474-0.0177-0.0645-0.12260.00560.00010.1538-0.0199-0.02920.1570.01480.1952-12.079310.534957.9082
40.67770.0995-0.35610.81110.53390.61340.0484-0.08390.05550.01070.0054-0.0329-0.0642-0.02940.00040.1017-0.01780.00070.1064-0.01070.1143-17.598817.13958.1002
50.65840.0280.5810.78660.57360.76750.07440.03290.0124-0.3046-0.0905-0.03-0.19550.0349-0.00150.1831-0.01580.00550.15720.00820.1656-17.589312.024645.9214
60.64630.1139-0.24660.22630.49462.2906-0.1016-0.1503-0.0391-0.0597-0.159-0.00160.3963-0.3178-0.30940.1669-0.0050.00150.177-0.01830.2003-27.562-1.667753.2441
70.9397-0.6827-0.1091.898-0.62610.92480.31830.4323-0.2281-0.7073-0.01760.2546-0.0211-0.12260.23830.17020.0098-0.01920.1699-0.04490.1795-22.93151.48239.4544
80.77520.37680.42610.76990.44380.32190.24670.1922-0.08350.2351-0.0412-0.36690.34170.05470.19240.15350.04980.04520.2313-0.01220.2122-13.1003-0.830749.7108
90.06750.05140.00610.17720.02630.2347-0.0542-0.12180.09070.0408-0.03570.08860.1867-0.073400.1829-0.01210.01950.1881-0.0240.1787-27.4873-6.319346.6577
100.6698-0.59390.28330.6148-0.42310.5662-0.5395-0.31410.2648-0.01730.2674-0.6874-0.5050.4888-0.05980.3234-0.1130.05660.333-0.08420.3674-24.016-4.485178.9542
110.5587-0.20160.22490.53520.04110.1738-0.33080.09590.01430.1045-0.1513-0.15050.076-0.20560.00030.1773-0.0245-0.02110.184-0.01310.1949-29.876-9.099681.2128
121.3989-0.0550.47850.77310.05090.88370.0067-0.0077-0.0451-0.0056-0.0258-0.06590.05910.070600.16380.00140.00090.13730.01810.1476-32.7764-19.571278.1986
130.60850.13250.16390.59940.16530.1243-0.01260.0524-0.13960.0017-0.01260.2722-0.0308-0.0174-0.00020.18920.01290.02930.16990.02060.1872-46.4509-19.853675.513
140.7459-0.40990.17530.4059-0.13080.0479-0.00030.01780.03520.06750.02720.0049-0.04040.095-00.1903-0.01780.00210.1472-0.00420.1368-41.7127-6.561674.7769
150.72460.1068-0.78170.5149-0.01971.6309-0.03020.29980.0003-0.10940.01970.33410.073-0.5879-0.12530.17470.0335-0.01310.21690.02030.2049-52.8669-6.651572.5795
160.1326-0.29280.02871.05850.11180.0425-0.0348-0.2481-0.13140.365-0.0788-0.1702-0.3704-0.2264-0.08370.22870.02440.03910.2063-0.03230.1082-42.0722-4.292882.6301
170.52680.11810.08940.35880.06220.1311-0.03330.10670.21850.0058-0.0848-0.2942-0.25890.2665-0.00560.2140.01730.02040.14940.00530.2009-46.67621.573669.234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 44 )A32 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 64 )A45 - 64
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 88 )A65 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 146 )A89 - 146
5X-RAY DIFFRACTION5chain 'A' and (resid 147 through 199 )A147 - 199
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 215 )A200 - 215
7X-RAY DIFFRACTION7chain 'A' and (resid 216 through 229 )A216 - 229
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 245 )A230 - 245
9X-RAY DIFFRACTION9chain 'A' and (resid 246 through 263 )A246 - 263
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 44 )B32 - 44
11X-RAY DIFFRACTION11chain 'B' and (resid 45 through 64 )B45 - 64
12X-RAY DIFFRACTION12chain 'B' and (resid 65 through 146 )B65 - 146
13X-RAY DIFFRACTION13chain 'B' and (resid 147 through 183 )B147 - 183
14X-RAY DIFFRACTION14chain 'B' and (resid 184 through 215 )B184 - 215
15X-RAY DIFFRACTION15chain 'B' and (resid 216 through 229 )B216 - 229
16X-RAY DIFFRACTION16chain 'B' and (resid 230 through 245 )B230 - 245
17X-RAY DIFFRACTION17chain 'B' and (resid 246 through 262 )B246 - 262

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