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- PDB-5n4t: VIM-2 metallo-beta-lactamase in complex with ((S)-3-mercapto-2-me... -

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Basic information

Entry
Database: PDB / ID: 5n4t
TitleVIM-2 metallo-beta-lactamase in complex with ((S)-3-mercapto-2-methylpropanoyl)-L-tryptophan (Compound 4)
ComponentsBeta-lactamase VIM-2
KeywordsHYDROLASE / metallo-beta-lactamase / inhibitor / complex / antibiotic resistance
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
BENZOIC ACID / FORMIC ACID / Chem-R59 / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.16 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 1.2Jan 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_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.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_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.ptnr3_label_seq_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 / _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)51,20915
Polymers49,8212
Non-polymers1,38813
Water11,187621
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A: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6278
Polymers24,9111
Non-polymers7177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5817
Polymers24,9111
Non-polymers6716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.903, 80.148, 79.085
Angle α, β, γ (deg.)90.000, 139.490, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-627-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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: 24910.648 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 / Details (production host): OPINF VECTOR BASED / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q9K2N0

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Non-polymers , 5 types, 634 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-R59 / (2~{S})-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


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
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: 0.92819 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: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.16→56.29 Å / Num. obs: 147820 / % possible obs: 99.96 % / Observed criterion σ(F): 0.117 / Observed criterion σ(I): 1.275 / Redundancy: 10.6 % / Biso Wilson estimate: 10.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Rsym value: 0.063 / Net I/σ(I): 10.3
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 6.51 % / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 10.25 / CC1/2: 0.998 / % possible all: 99.96

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.01 Å56.29 Å
Translation5.01 Å56.29 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c1d

4c1d


Resolution: 1.16→56.288 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.67
RfactorNum. reflection% reflection
Rfree0.1955 7266 4.97 %
Rwork0.1745 --
obs0.1755 146186 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.84 Å2 / Biso mean: 20.2636 Å2 / Biso min: 5.89 Å2
Refinement stepCycle: final / Resolution: 1.16→56.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 78 632 4204
Biso mean--25.66 32.69 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133944
X-RAY DIFFRACTIONf_angle_d1.1785427
X-RAY DIFFRACTIONf_chiral_restr0.091606
X-RAY DIFFRACTIONf_plane_restr0.009729
X-RAY DIFFRACTIONf_dihedral_angle_d13.6911391
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 (%)
1.16-1.17320.40222720.38824406467895
1.1732-1.1870.4063030.39124444474796
1.187-1.20150.38242720.37224438471097
1.2015-1.21670.40932310.36224566479797
1.2167-1.23270.37882560.36474581483798
1.2327-1.24960.37712380.35794502474098
1.2496-1.26740.35822530.35154539479298
1.2674-1.28630.30092250.33964627485298
1.2863-1.30640.352220.32844619484198
1.3064-1.32790.32362200.30754644486499
1.3279-1.35080.31122350.29244596483199
1.3508-1.37530.27772510.28254643489499
1.3753-1.40180.28782500.27064603485399
1.4018-1.43040.29512270.25174665489299
1.4304-1.46150.28462110.24724685489699
1.4615-1.49550.24472390.22784634487399
1.4955-1.53290.24352030.21264694489799
1.5329-1.57440.23472530.19774649490299
1.5744-1.62070.2072390.174646734912100
1.6207-1.6730.18912710.16846504921100
1.673-1.73280.17482460.150346454891100
1.7328-1.80220.17082510.144146804931100
1.8022-1.88420.16182220.136647054927100
1.8842-1.98350.16282120.13647134925100
1.9835-2.10780.15232420.127846904932100
2.1078-2.27060.14132250.127647074932100
2.2706-2.49910.14152270.121847134940100
2.4991-2.86070.1352460.120747384984100
2.8607-3.60410.143040.122646484952100
3.6041-56.3540.15512200.134448235043100
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)
13.4614-1.0025-2.37941.68340.79964.0855-0.0361-0.04440.11040.10220.00240.0118-0.0138-0.06570.03950.07990.0121-0.01510.0552-0.00650.100466.733621.454651.7452
22.7898-1.0331-1.362.29392.16225.25150.03850.0560.3349-0.00460.0156-0.1037-0.27050.0064-0.06880.09320.0018-0.01280.03950.0140.154970.008128.376547.9702
32.3897-1.5019-0.2262.0937-0.42890.7894-0.01430.01460.3390.038-0.0133-0.4008-0.07990.1169-0.04090.0924-0.0044-0.00530.1087-0.00440.205477.836224.922347.6469
41.3666-0.3515-0.29581.41320.03181.2189-0.0577-0.19420.14240.20140.0524-0.23420.01340.13590.03410.09280.0177-0.03480.0933-0.01220.102877.446315.138854.2404
54.46464.8063-4.62045.2992-4.72536.3606-0.20290.4118-0.0773-0.3510.170.0170.3226-0.3299-0.00270.12170.0250.01750.113-0.01220.118871.46884.418242.2281
65.21490.14761.90272.68750.4517.224-0.0389-0.0438-0.03870.0850.0039-0.36750.24610.46190.00460.08350.03590.0010.07950.00970.143684.53857.442247.7967
76.35110.68773.24691.1150.45924.6782-0.0122-0.4014-0.25440.28120.0415-0.0770.197-0.1349-0.03390.13860.02340.0040.08640.01380.079472.60815.323956.7002
83.7981-0.167-1.97912.40742.24669.6070.02420.1503-0.2003-0.06320.0603-0.18960.05190.0455-0.09290.11580.01650.02440.07260.00280.158478.1589-0.282943.3621
95.4123-1.5521.48137.4344-1.86792.95590.1323-0.89450.8590.9483-0.0184-0.6319-0.8557-0.5836-0.00390.40470.01490.10770.3194-0.08430.253444.83451.314541.9397
103.1820.4840.18973.63320.1923.42490.143-0.27550.16740.2129-0.07490.1003-0.2156-0.2279-0.04080.1034-0.0180.02720.13980.0080.066543.8974-6.341133.8675
115.5563-0.5471-0.04193.3611-0.34592.65220.0487-0.44530.00250.5181-0.00030.3341-0.1708-0.1426-0.05650.2239-0.08260.01920.25810.02680.090440.9976-11.633341.6799
121.30650.3026-0.9772.0825-0.45851.94130.1183-0.1903-0.07310.1458-0.0844-0.00230.0961-0.1183-0.0070.1004-0.0286-0.01520.10820.02480.064248.1858-13.565431.3343
133.37741.2036-1.02632.8778-1.12584.04260.0652-0.2313-0.42320.1621-0.1066-0.46250.23470.15510.04910.1481-0.0107-0.03410.07780.03030.165253.5738-20.206429.6661
141.45250.5941-0.36321.9008-0.11531.064-0.02370.0782-0.0739-0.14850.0105-0.07540.0913-0.09460.00730.0846-0.00150.00150.07940.00070.055849.6741-11.295120.036
157.3933-6.1962-1.84659.2453.00251.0282-0.1707-0.40530.12450.3230.1958-0.3654-0.05090.2465-0.01410.1326-0.01190.00980.13520.03410.093558.40073.327227.3899
163.68332.15862.90073.05010.90225.1122-0.0880.43250.2042-0.36360.0831-0.0547-0.17790.09290.04470.13930.00310.03430.09270.01870.081555.3703-0.493813.7037
173.60340.31382.95841.64370.46917.3058-0.0376-0.0390.2891-0.0701-0.04240.2498-0.3184-0.30440.08520.08320.01990.01070.08790.01540.11644.44542.078323.6585
187.54752.27690.36634.61440.04154.0675-0.1120.0062-0.1079-0.11020.0889-0.1832-0.22510.20990.02460.1125-0.00520.02250.0554-0.00160.065158.39347.894420.0946
196.0516-0.63322.28885.7753-2.35437.1755-0.055-0.2477-0.69940.00140.2080.48230.4857-0.7304-0.11470.1746-0.02880.07870.22990.0120.254157.95598.159656.932
202.8324-0.2504-0.16553.42710.15342.4895-0.0412-0.0377-0.03680.09850.00620.07950.0762-0.22320.03760.07110.01010.00680.1024-0.01330.071163.366315.842154.8044
214.8388-1.0373-1.99585.6086-1.54855.1624-0.1002-0.1224-0.07830.34930.10050.35160.0307-0.3921-0.00990.09030.0150.02440.1576-0.03530.143554.944720.584757.502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 103 through 122 )B103 - 122
2X-RAY DIFFRACTION2chain 'B' and (resid 123 through 145 )B123 - 145
3X-RAY DIFFRACTION3chain 'B' and (resid 146 through 163 )B146 - 163
4X-RAY DIFFRACTION4chain 'B' and (resid 164 through 199 )B164 - 199
5X-RAY DIFFRACTION5chain 'B' and (resid 200 through 215 )B200 - 215
6X-RAY DIFFRACTION6chain 'B' and (resid 216 through 229 )B216 - 229
7X-RAY DIFFRACTION7chain 'B' and (resid 230 through 245 )B230 - 245
8X-RAY DIFFRACTION8chain 'B' and (resid 246 through 263 )B246 - 263
9X-RAY DIFFRACTION9chain 'A' and (resid 30 through 44 )A30 - 44
10X-RAY DIFFRACTION10chain 'A' and (resid 45 through 88 )A45 - 88
11X-RAY DIFFRACTION11chain 'A' and (resid 89 through 102 )A89 - 102
12X-RAY DIFFRACTION12chain 'A' and (resid 103 through 122 )A103 - 122
13X-RAY DIFFRACTION13chain 'A' and (resid 123 through 146 )A123 - 146
14X-RAY DIFFRACTION14chain 'A' and (resid 147 through 199 )A147 - 199
15X-RAY DIFFRACTION15chain 'A' and (resid 200 through 215 )A200 - 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 263 )A246 - 263
19X-RAY DIFFRACTION19chain 'B' and (resid 31 through 52 )B31 - 52
20X-RAY DIFFRACTION20chain 'B' and (resid 53 through 88 )B53 - 88
21X-RAY DIFFRACTION21chain 'B' and (resid 89 through 102 )B89 - 102

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