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- PDB-5nai: mono-Zinc VIM-5 metallo-beta-lactamase in complex with (1-chloro-... -

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Basic information

Entry
Database: PDB / ID: 5nai
Titlemono-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 / hydrolase activity / 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 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-93W / FLUORIDE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 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 28, 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 / struct_conn_type
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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_label_seq_id / _struct_conn_type.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8378
Polymers28,1001
Non-polymers7367
Water5,008278
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-102 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.553, 67.555, 40.093
Angle α, β, γ (deg.)90.00, 92.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 28100.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaVIM-5 / Plasmid: open vector based / Details (production host): plasmid derived / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8GKX2

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Non-polymers , 5 types, 285 molecules

#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.: 1 / Source method: obtained synthetically / Formula: C21H16ClN3O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 1.91 Å3/Da / Density % sol: 35.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium fluoride, 0.1 M Bis-Tris propane, 20% (w/v) Polyethylene glycol 3350, pH=8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 74624 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.8
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 6 % / Rmerge(I) obs: 0.398 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.15 Å40.05 Å
Translation1.15 Å40.05 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: 1.15→3.89 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.141 1950 2.69 %
Rwork0.131 --
obs0.131 72606 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.05 Å2
Refinement stepCycle: LAST / Resolution: 1.15→3.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 40 278 2031
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)
11.6840.0023-0.64965.42870.95142.3244-0.0187-0.0128-0.12820.1436-0.15060.43820.1928-0.24490.17080.1295-0.02220.02660.1942-0.02360.20213.5907-8.70437.9717
21.4389-0.3464-0.14212.9584-0.52631.9457-0.02180.05360.0064-0.00350.02660.06550.0543-0.04090.00530.0906-0.007-0.00140.1083-0.00620.113710.9208-5.82462.4834
34.3679-3.71340.44364.92190.33612.0851-0.00290.0739-0.27940.0285-0.0030.38590.1009-0.28810.01890.1323-0.02960.00060.1820.0030.16763.3756-8.5-3.4842
41.10120.37180.03421.0267-0.00821.1096-0.03460.0998-0.0366-0.06360.048-0.06270.0350.0192-0.01850.1345-0.0030.00370.13760.00170.131121.1708-2.0654-4.4392
51.98520.55510.61820.7674-0.34962.2592-0.0617-0.05610.12970.04260.0303-0.0724-0.08450.08870.05130.1239-0.00690.00310.13330.00020.136522.79895.13134.2613
61.0390.80260.06490.6975-0.31741.7524-0.0127-0.05990.02470.127-0.0124-0.06950.01150.05920.0220.14640.0020.00660.1347-0.01650.135518.8267-1.149611.4556
78.1002-4.4302-0.87032.59161.14943.07560.0003-0.44690.44530.3295-0.0184-0.4088-0.16560.22570.09050.1874-0.0369-0.01430.2006-0.00360.17427.30943.993815.6001
81.73131.3160.07945.30950.73141.86130.0727-0.25770.25130.1736-0.06380.1628-0.101-0.11780.00460.14890.010.00570.1747-0.02910.152513.03711.896914.2338
95.9621-0.29741.56254.7285-0.91665.89570.0714-0.2115-0.06280.0675-0.1617-0.24840.21060.24330.09110.1683-0.00550.00350.16710.00510.119323.7447-3.464521.578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 31 THROUGH 52 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 53 THROUGH 88 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 89 THROUGH 102 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 103 THROUGH 163 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 164 THROUGH 183 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 184 THROUGH 215 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 216 THROUGH 229 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 230 THROUGH 245 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 246 THROUGH 261 )

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