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- PDB-5n58: di-Zinc VIM-5 metallo-beta-lactamase in complex with (1-chloro-4-... -

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Basic information

Entry
Database: PDB / ID: 5n58
Titledi-Zinc VIM-5 metallo-beta-lactamase in complex with (1-chloro-4-hydroxyisoquinoline-3-carbonyl)-D-tryptophan (Compound 1)
ComponentsClass B metallo-beta-lactamase
KeywordsHYDROLASE / metallo-beta-lactamase / inhibitor / complex / antibiotic resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / metal ion binding
Similarity search - Function
: / : / : / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...: / : / : / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-93W / beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.957 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 13, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class B metallo-beta-lactamase
B: Class B metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3379
Polymers56,1372
Non-polymers1,2007
Water3,891216
1
A: Class B metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7936
Polymers28,0681
Non-polymers7255
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class B metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5443
Polymers28,0681
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.471, 81.540, 95.892
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Class B metallo-beta-lactamase / Meta-beta-carbapenem / Metallo-beta-lactamase


Mass: 28068.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaVIM-5 / Plasmid: opinf vector based / Details (production host): plasmid derived / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q8GKX2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-93W / (2~{R})-2-[(1-chloranyl-4-oxidanyl-isoquinolin-3-yl)carbonylamino]-3-(1~{H}-indol-3-yl)propanoic acid


Mass: 409.822 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H16ClN3O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 1.9 Å3/Da / Density % sol: 35.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane, 20% (w/v) Polyethylene glycol 3350,pH=6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.957→81.54 Å / Num. obs: 31417 / % possible obs: 99.7 % / Redundancy: 2.2 % / Biso Wilson estimate: 25.27 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 14.3
Reflection shellResolution: 1.957→2.027 Å / Rmerge(I) obs: 0.152 / Num. unique obs: 3085 / Rpim(I) all: 0.062 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.05 Å62.12 Å
Translation5.05 Å62.12 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A87

5a87


Resolution: 1.957→62.118 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 1999 6.4 %
Rwork0.1874 29257 -
obs0.1906 31256 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.87 Å2 / Biso mean: 33.7312 Å2 / Biso min: 13.84 Å2
Refinement stepCycle: final / Resolution: 1.957→62.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 73 216 3498
Biso mean--45.31 39.36 -
Num. residues----441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163365
X-RAY DIFFRACTIONf_angle_d1.0754602
X-RAY DIFFRACTIONf_chiral_restr0.067529
X-RAY DIFFRACTIONf_plane_restr0.008603
X-RAY DIFFRACTIONf_dihedral_angle_d16.2611913
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9569-2.00590.32051410.251620622203100
2.0059-2.06010.3171400.24482051219199
2.0601-2.12070.31211420.224720752217100
2.1207-2.18920.29221390.20992024216398
2.1892-2.26740.27351420.200620862228100
2.2674-2.35820.23891410.212520632204100
2.3582-2.46550.2351420.18472089223199
2.4655-2.59550.27681440.186620872231100
2.5955-2.75810.26381410.174220732214100
2.7581-2.97110.23461440.178621062250100
2.9711-3.27010.21471450.1632115226099
3.2701-3.74320.20761420.15442083222599
3.7432-4.71580.19671430.15972082222596
4.7158-62.14970.22831530.21552261241499
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)
15.3746-1.08896.24642.6241-0.52127.7990.08220.89360.1394-0.4718-0.12660.01880.00720.28880.09920.2649-0.01130.01460.32860.01180.231710.1326-25.1803-25.078
24.6575-1.22371.76913.3874-1.39923.7236-0.02790.2552-0.0116-0.0275-0.08420.06670.0425-0.14420.08410.14570.00090.03040.1951-0.01760.11264.3347-27.1228-20.9064
34.1558-6.2414-3.44239.46424.98623.24070.02240.23050.0412-0.1316-0.06520.07820.0268-0.1690.03970.1423-0.02140.0130.1939-0.00620.18481.0012-27.3622-14.0953
47.6027-3.9492-2.90927.80582.98124.7371-0.07120.007-0.0755-0.02860.11940.27350.0228-0.1557-0.0140.1563-0.04450.0140.18030.01660.1359-6.1079-28.7545-9.0601
53.86790.141-0.16553.03740.49620.95010.0483-0.27450.16870.1778-0.11250.06420.025-0.12930.05680.19910.00230.00410.2768-0.01130.13311.7578-21.8503-3.6213
61.40530.5768-0.77062.8857-1.00433.2259-0.03030.03670.3054-0.07680.16690.3091-0.2211-0.3479-0.09180.1834-0.0031-0.02260.1827-0.00470.1826.7496-13.5912-13.0174
75.0932-5.54323.55127.8046-2.41526.3747-0.0519-0.59810.42950.19510.046-0.0124-0.49980.14580.05050.2421-0.05890.00810.2066-0.04470.20137.1598-7.527-3.7797
86.10420.76422.26282.59580.0695.73840.1694-0.0301-0.03750.09420.03240.0913-0.10780.4619-0.19850.179-0.02850.02250.18550.01490.148714.2861-15.0273-14.0411
93.3867-5.15633.44488.8204-3.29177.7283-0.2886-0.1350.84220.23140.349-0.3391-0.94840.2710.00080.3472-0.0240.02910.2130.00690.26429.3783-3.7723-12.8882
105.50180.47523.64332.2572-0.40852.6461-0.0040.1067-0.034-0.18950.03560.221-0.1463-0.1581-0.12040.16170.00740.00520.242-0.0160.221520.1947-13.8464-31.6741
116.4797-1.29142.48683.4469-1.78032.0732-0.036-0.06440.2661-0.06750.11460.332-0.09330.1093-0.03530.1851-0.0230.00420.20510.01670.265125.3207-6.5826-30.8659
123.1036-1.7082-2.00236.7981.46852.747-0.04270.20910.0228-0.3772-0.0897-0.01540.10420.11410.10980.1749-0.0272-0.00450.2267-0.00370.17336.0132-12.255-37.6961
135.12161.02730.6622.42240.63411.8227-0.0595-0.2142-0.3293-0.2293-0.0034-0.10240.15880.05450.03870.21890.03260.03450.17150.04720.172429.1879-28.0572-32.4846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 52 )A39 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 102 )A53 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 122 )A103 - 122
4X-RAY DIFFRACTION4chain 'A' and (resid 123 through 146 )A123 - 146
5X-RAY DIFFRACTION5chain 'A' and (resid 147 through 184 )A147 - 184
6X-RAY DIFFRACTION6chain 'A' and (resid 185 through 215 )A185 - 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 258 )A246 - 258
10X-RAY DIFFRACTION10chain 'B' and (resid 39 through 76 )B39 - 76
11X-RAY DIFFRACTION11chain 'B' and (resid 77 through 102 )B77 - 102
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 163 )B103 - 163
13X-RAY DIFFRACTION13chain 'B' and (resid 164 through 259 )B164 - 259

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