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- PDB-6rpn: Structure of metallo beta lactamase VIM-2 with cyclic boronate APC308. -

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Basic information

Entry
Database: PDB / ID: 6rpn
TitleStructure of metallo beta lactamase VIM-2 with cyclic boronate APC308.
ComponentsBeta-lactamase VIM-2
KeywordsANTIMICROBIAL PROTEIN / beta lactamases / antimicrobial resistance / cyclic boronate
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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-KDZ / Chem-KL8 / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.409 Å
AuthorsParkova, A. / Lucic, A. / Brem, J. / McDonough, M.A. / Langley, G.W. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Broad Spectrum beta-Lactamase Inhibition by a Thioether Substituted Bicyclic Boronate.
Authors: Parkova, A. / Lucic, A. / Krajnc, A. / Brem, J. / Calvopina, K. / Langley, G.W. / McDonough, M.A. / Trapencieris, P. / Schofield, C.J.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 2.0Apr 15, 2020Group: Non-polymer description / Refinement description / Category: chem_comp / refine / Item: _chem_comp.formula / _refine.pdbx_diffrn_id
Revision 2.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2Jan 24, 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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)53,38719
Polymers51,3872
Non-polymers2,00017
Water12,520695
1
A: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6238
Polymers25,6931
Non-polymers9297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,76411
Polymers25,6931
Non-polymers1,07010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.081, 79.155, 67.746
Angle α, β, γ (deg.)90.000, 130.030, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

21A-742-

HOH

31B-763-

HOH

41B-896-

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 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.: 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: pOPINF / Production host: Escherichia coli (E. coli) / Variant (production host): Lemo21 / References: UniProt: Q9K2N0

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Non-polymers , 7 types, 712 molecules

#2: Chemical ChemComp-KDZ / (3~{R})-2,2-bis(oxidanyl)-3-(phenylmethylsulfanyl)-3,4-dihydro-1,2-benzoxaborinin-2-ium-8-carboxylic acid


Mass: 331.171 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C16H16BO5S
#3: Chemical ChemComp-KL8 / (3~{S})-2,2-bis(oxidanyl)-3-(phenylmethylsulfanyl)-3,4-dihydro-1,2-benzoxaborinin-2-ium-8-carboxylic acid


Mass: 331.171 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C16H16BO5S
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.07 Å3/Da / Density % sol: 40.52 % / Description: Rod shaped crystal about 100 microns big.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.25
Details: 0.2M Magnesium Chloride, 25% PEG 8000, 0.1M Tris Buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 8, 2019 / Details: OSMIC VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. obs: 75121 / % possible obs: 95.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.063 / Rrim(I) all: 0.106 / Χ2: 1.097 / Net I/σ(I): 14.4 / Num. measured all: 147264
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.41-1.461.40.36566820.7250.3650.5171.15285.1
1.46-1.521.50.28768850.7980.2870.4061.1588.1
1.52-1.591.50.22971460.8670.2290.3241.16391.2
1.59-1.671.60.18773870.9010.1870.2641.10394.4
1.67-1.781.60.14676730.9350.1460.2061.13797.4
1.78-1.911.70.10877550.9650.1080.1521.04699.1
1.91-2.111.80.09178650.9710.0840.1251.38999.9
2.11-2.412.20.10578630.9690.0850.1361.007100
2.41-3.042.50.09578760.9720.0720.1191.028100
3.04-503.50.06979890.990.0440.0821.05399.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.7 Å29.19 Å
Translation5.7 Å29.19 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-20002.3.10data reduction
HKL-20002.3.10data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ3

4bz3


Resolution: 1.409→31.336 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1556 1843 2.45 %
Rwork0.1288 73271 -
obs0.1294 75114 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.95 Å2 / Biso mean: 15.495 Å2 / Biso min: 3.26 Å2
Refinement stepCycle: final / Resolution: 1.409→31.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 110 718 4315
Biso mean--21.82 28.36 -
Num. residues----466
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4093-1.44740.27741170.23114944506184
1.4474-1.490.23551380.2075126526487
1.49-1.53810.24081250.18495266539190
1.5381-1.59310.18251370.16945361549892
1.5931-1.65690.19691500.15325558570894
1.6569-1.73230.15761380.13885717585597
1.7323-1.82360.17311470.1295804595198
1.8236-1.93780.16431500.12355866601699
1.9378-2.08740.15061470.111558656012100
2.0874-2.29740.13771460.112259166062100
2.2974-2.62970.14811490.109558976046100
2.6297-3.31260.1251490.111859356084100
3.3126-31.34360.13441500.122160166166100
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)
14.3871-0.2706-3.68392.17690.49034.2020.1271-0.30570.51250.0467-0.01150.0469-0.35610.2504-0.18650.1236-0.0058-0.03140.1386-0.06010.1629-26.9112-5.152483.9696
22.44330.6336-0.42412.8738-0.64392.2767-0.0623-0.07380.0930.00580.0759-0.01170.04650.0719-0.01040.04160.017-0.01180.0497-0.00910.0582-31.1817-12.984980.2241
31.9906-1.14761.00434.8361.03252.3942-0.1051-0.13850.13270.16450.0498-0.2302-0.09350.32950.01540.06160.0026-0.01540.1028-0.01020.0987-22.9482-16.93783.771
42.4402-0.65922.17111.3681-0.41884.5167-0.0547-0.0618-0.01090.04530.0338-0.02320.0091-0.00680.03250.06150.01130.01730.0416-0.00660.0648-34.1858-19.320978.7419
54.7189-0.42731.19271.46580.64372.8255-0.05410.1338-0.1341-0.04650.0189-0.03280.09470.03910.01430.0874-0.00870.02510.02350.00170.0744-36.5748-25.958573.0572
62.5994-2.6201-0.15972.9370.60871.2339-0.01520.0407-0.3131-0.02580.01810.20610.0622-0.0178-0.00350.0699-0.016-0.00030.0611-0.00750.0611-44.7247-24.055474.4383
70.8093-0.1590.27721.4812-0.30551.45880.0016-0.01230.03380.0004-0.00330.0794-0.0423-0.0724-0.00060.04960.00380.01150.0548-0.00580.0608-45.7306-9.871275.9409
87.24841.381-3.97930.3816-1.12933.48820.0485-0.26140.19420.0863-0.03060.042-0.08560.0747-0.03590.09220.00920.00910.0656-0.01550.0796-41.6428-4.1183.0994
93.50780.3271.95563.7933-1.8982.80120.00480.24330.1731-0.1598-0.00850.0401-0.1195-0.10760.01460.07120.0187-0.00170.06980.01190.1006-46.61411.338869.2592
104.53752.1296-1.64726.8449-3.21216.67770.0703-0.3242-0.41360.1043-0.1201-0.06240.28220.22290.03070.0890.0272-0.05510.10930.02440.121-10.32811.400865.3354
117.00511.3205-3.36822.1307-0.88363.70950.0235-0.12-0.05320.06590.0530.11170.117-0.1034-0.01440.0772-0.0072-0.01750.05950.02280.0548-17.81065.625762.6319
121.09550.07980.46860.7260.10831.4746-0.00760.01580.0301-0.0022-0.0086-0.0614-0.06580.06640.01850.0627-0.00370.01090.04930.0020.0591-16.873514.485353.2017
132.5003-1.07221.18873.0032-0.36171.23520.1066-0.0072-0.19680.09220.00070.06410.1651-0.1611-0.08970.0989-0.022-0.02220.0632-0.01910.0751-25.346-0.60247.7236
141.520.8289-0.2891.75290.17682.29770.04080.0683-0.0636-0.00350.0126-0.04890.21960.0157-0.04360.12420.0236-0.01660.0428-0.00630.079-20.6028-4.188748.7201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 52 )A31 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 88 )A53 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 102 )A89 - 102
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 122 )A103 - 122
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 146 )A123 - 146
6X-RAY DIFFRACTION6chain 'A' and (resid 147 through 163 )A147 - 163
7X-RAY DIFFRACTION7chain 'A' and (resid 164 through 229 )A164 - 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 31 through 52 )B31 - 52
11X-RAY DIFFRACTION11chain 'B' and (resid 53 through 76 )B53 - 76
12X-RAY DIFFRACTION12chain 'B' and (resid 77 through 199 )B77 - 199
13X-RAY DIFFRACTION13chain 'B' and (resid 200 through 229 )B200 - 229
14X-RAY DIFFRACTION14chain 'B' and (resid 230 through 263 )B230 - 263

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