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- PDB-8pjm: Metallo beta-lactamase VIM2 with compound AK110 -

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Basic information

Entry
Database: PDB / ID: 8pjm
TitleMetallo beta-lactamase VIM2 with compound AK110
ComponentsBeta-lactamase VIM-2
KeywordsANTIBIOTIC / HYDROLASE / HYDROLASES / Metallo Beta Lactamase / 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
Similarity search - Domain/homology
: / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsLucic, A. / Hinchliffe, P. / Schofield, C.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
Citation
Journal: To Be Published
Title: Metallo beta-lactamase VIM2 with compound AK110
Authors: Kranjc, A. / Lucic, A. / Schofield, C.
#1: Journal: Methods / Year: 2011
Title: Automated data collection for macromolecular crystallography.
Authors: Winter, G. / McAuley, K.E.
History
DepositionJun 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 2.0May 1, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct / struct_asym / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.id / _citation.title / _citation_author.citation_id / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.number_obs / _reflns_shell.number_unique_obs / _struct.title / _struct_asym.entity_id
Description: Ligand identity
Details: The previous submission contained the wrong ligand-this was spotted, but not properly fixed due to confusion on our side.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAAA: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3329
Polymers25,6931
Non-polymers6398
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-143 kcal/mol
Surface area9430 Å2
Unit cell
Length a, b, c (Å)63.653, 74.086, 78.739
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11AAAA-407-

HOH

21AAAA-611-

HOH

31AAAA-639-

HOH

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Components

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Protein , 1 types, 1 molecules AAAA

#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 VIM-2 / Metallo-beta-lactamase vim-2 / Mettalo-beta-lactamase VIM-2 / VIM-2 metallo-beta-lactamase / VIM-2 protein


Mass: 25693.488 Da / Num. of mol.: 1
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
Production host: Escherichia coli (E. coli) / References: UniProt: Q9K2N0

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Non-polymers , 5 types, 254 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-A1H7J / ~{N}-[[(3~{R})-1,1-bis(oxidanyl)-3~{H}-2,1$l^{4}-benzoxaborol-3-yl]methyl]pyrrolidine-1-sulfonamide


Mass: 313.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18BN2O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.81 Å3/Da / Density % sol: 31.91 % / Description: Crystal size 100x50x75 um
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MAGNESIUM FORMATE, 20 % W/V

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.44→29.66 Å / Num. obs: 34084 / % possible obs: 99.97 % / Redundancy: 13.2 % / Biso Wilson estimate: 13.73 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.086 / Net I/σ(I): 20.2
Reflection shellResolution: 1.44→1.491 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 3 / Num. unique obs: 3339 / CC1/2: 0.9 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→29.66 Å / SU ML: 0.1018 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.1082
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1559 2007 5.89 %
Rwork0.1303 32076 -
obs0.1318 34083 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.21 Å2
Refinement stepCycle: LAST / Resolution: 1.44→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 28 246 2018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081930
X-RAY DIFFRACTIONf_angle_d1.0112665
X-RAY DIFFRACTIONf_chiral_restr0.0781297
X-RAY DIFFRACTIONf_plane_restr0.0092360
X-RAY DIFFRACTIONf_dihedral_angle_d12.4769712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.470.20671380.17982212X-RAY DIFFRACTION98.29
1.47-1.510.22121420.16752270X-RAY DIFFRACTION100
1.51-1.560.18791520.15272255X-RAY DIFFRACTION100
1.56-1.610.18591330.1482293X-RAY DIFFRACTION100
1.61-1.670.16811350.1422254X-RAY DIFFRACTION100
1.67-1.730.18021450.13592274X-RAY DIFFRACTION100
1.73-1.810.16931490.13312277X-RAY DIFFRACTION100
1.81-1.910.15931360.12382288X-RAY DIFFRACTION100
1.91-2.030.15981520.11862279X-RAY DIFFRACTION100
2.03-2.180.15071370.11742287X-RAY DIFFRACTION100
2.18-2.40.15441480.11672306X-RAY DIFFRACTION100
2.4-2.750.14511410.12032310X-RAY DIFFRACTION100
2.75-3.470.1461440.11982333X-RAY DIFFRACTION100
3.47-29.660.14051550.13972438X-RAY DIFFRACTION99.96
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)
10.4736379823660.216459626036-0.8033141938430.910484409442-0.9097696175673.341739113930.035395164501-0.1479061172420.5956406224250.3060850553040.0759470131657-0.0532516773805-0.33311806828-0.358132318360.2248116810890.2503654432280.01647781440830.02160333981980.181465138314-0.05324737612770.20980484069-23.4717908063-3.54827653932-2.96417029843
23.14281691727-0.148859627924-0.8305916297761.341324090340.09037032142272.451034492190.0286492989728-0.2910680178890.1771453616240.1693683845250.0824857258006-0.136209189886-0.1060904797690.159434188483-0.01477680394070.1425125444110.011190795985-0.0002089354170150.129502827387-0.0396898256080.134283746507-18.2532160376-7.70206474632-7.05072375893
31.99342334357-0.162614337894-0.5383054522091.166087379390.2480111436211.659422347080.0384742235144-0.003637922744110.1089946306120.009351227150320.0371961432178-0.0775098376705-0.03390392454150.10785537485-0.0188753446890.0923418276659-0.00678974150270.001237077350510.0859516769413-0.01093469028440.0893355806423-16.4130279693-10.1860022392-13.0266575947
41.934587718470.2783404943540.574411117831.705622841010.5165177059292.07398706246-0.00902239261844-0.1213434569750.3743055696260.04909427245890.03825241431970.0159986896414-0.3228764682340.01540521240320.004645213349210.1017627921550.01028625922640.02032336625540.0568422252023-0.0025650760220.107459733679-19.93164943-0.919302889836-14.9001208334
51.194435968520.0298336004744-0.2939311322951.30688947363-0.309353472341.470057456780.03329828124190.0319347093551-0.0649279162813-0.07530702262410.00229779617105-0.002740460780520.05888253087930.063956217067-0.03160391046860.06883404517410.0101567912966-9.58700105814E-50.0817824408521-0.01463561195070.0724031476762-15.8771484894-19.8412764587-17.6066475656
60.3704184118450.6828191665060.5675983685282.672663929072.557604712323.90186046450.000978172984824-0.242688223553-0.1035951068320.182052744128-0.2307494314620.513394157916-0.00697172337358-0.4888082704860.05540321485460.1539221908930.01080877443250.01582787823140.1876779652550.01210676520670.213470471724-24.0829805789-23.5815278973-0.85201430271
74.62877990326-0.07390968587220.6375036399393.95557609888-0.05606742673032.773079742750.0118902764613-0.0769305263729-0.293235337970.289046301951-0.0120960308442-0.4251173539180.3597668235120.5498089052640.005868165137230.184265391380.0613259459115-0.02549220209920.186698428430.03135575400140.168196726818-11.7424385248-31.0899298861-3.60841802643
81.49809479048-0.8495497322820.1056540216252.27252870229-0.1953922937210.0176980813852-0.0145745174748-0.20016162143-0.003767731609040.260566382940.0250425909632-0.246868068214-0.06094952138820.331913499370.04396470780890.130859745468-0.0201118176839-0.02728357950710.255067638531-0.001085237158150.102355277733-10.488625931-16.9141367176-2.05773823456
95.618562228861.79058672624-0.3242297605435.28555277351-0.7483122511123.61095002702-0.121757184608-0.200577208025-0.407508944162-0.009557139884560.06684654524060.03153051810770.289428990127-0.01701208407630.02448404114270.1813134292410.0226054334615-0.002984620375390.1579086239190.0169360856750.121989386833-18.7611551804-27.72109507644.20665627852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsLabel asym-IDLabel seq-ID
1X-RAY DIFFRACTION1{A|32-44 }A1 - 13
2X-RAY DIFFRACTION2{A|45-64 }A14 - 33
3X-RAY DIFFRACTION3{A|65-88 }A34 - 57
4X-RAY DIFFRACTION4{A|89-102 }A58 - 71
5X-RAY DIFFRACTION5{A|103-199 }A72 - 168
6X-RAY DIFFRACTION6{A|200-215 }A169 - 184
7X-RAY DIFFRACTION7{A|216-229 }A185 - 198
8X-RAY DIFFRACTION8{A|230-245 }A199 - 214
9X-RAY DIFFRACTION9{A|246-263 }A215 - 232

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