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- PDB-5k48: VIM-2 Metallo Beta Lactamase in complex with 3-(mercaptomethyl)-[... -

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Basic information

Entry
Database: PDB / ID: 5k48
TitleVIM-2 Metallo Beta Lactamase in complex with 3-(mercaptomethyl)-[1,1'-biphenyl]-4-carboxylic acid
ComponentsBeta-lactamase VIM-2
KeywordsHYDROLASE / metallo beta-lactamase / antibiotic resistance / carbapenamase. inhibitor
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
FORMIC ACID / 4-phenyl-2-(sulfanylmethyl)benzoic acid / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.744 Å
AuthorsZollman, D. / McDonough, M. / Brem, J. / Schofield, C.
CitationJournal: J. Med. Chem. / Year: 2018
Title: In Silico Fragment-Based Design Identifies Subfamily B1 Metallo-beta-lactamase Inhibitors.
Authors: Cain, R. / Brem, J. / Zollman, D. / McDonough, M.A. / Johnson, R.M. / Spencer, J. / Makena, A. / Abboud, M.I. / Cahill, S. / Lee, S.Y. / McHugh, P.J. / Schofield, C.J. / Fishwick, C.W.G.
History
DepositionMay 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 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_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.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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_seq_id / _struct_conn.ptnr2_label_asym_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)52,49815
Polymers51,3872
Non-polymers1,11113
Water6,900383
1
A: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2728
Polymers25,6931
Non-polymers5797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2267
Polymers25,6931
Non-polymers5336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.888, 79.542, 67.892
Angle α, β, γ (deg.)90.000, 130.600, 90.000
Int Tables number5
Space group name H-MC121

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Components

#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: OPINF / Details (production host): VECTOR BASED ON PTRIEX VECTOR / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K2N0
#2: Chemical ChemComp-S5Z / 4-phenyl-2-(sulfanylmethyl)benzoic acid


Mass: 244.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H12O2S
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: CH2O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MAGNESIUM FORMATE, 20 % W/V PEG3350, 1 MM TCEP, 213 uM protein, 12.5 uM inhibitor.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.542 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 29, 2013 / Details: Osmic HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.744→50 Å / Num. obs: 40087 / % possible obs: 95 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.079 / Net I/av σ(I): 12.239 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.75-1.8120.3891.875185.1
1.81-1.892.20.329189.8
1.89-1.972.60.264193.1
1.97-2.072.90.213194.9
2.07-2.23.40.2196.1
2.2-2.383.60.161197
2.38-2.613.60.117197.7
2.61-2.993.60.085198.1
2.99-3.773.60.063199.1
3.77-503.50.038199.3

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C1D

4c1d


Resolution: 1.744→25.819 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.98
RfactorNum. reflection% reflection
Rfree0.1936 2015 5.03 %
Rwork0.1658 --
obs0.1673 40076 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.64 Å2 / Biso mean: 27.6485 Å2 / Biso min: 9.92 Å2
Refinement stepCycle: final / Resolution: 1.744→25.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3474 0 55 383 3912
Biso mean--30.37 34.6 -
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033672
X-RAY DIFFRACTIONf_angle_d0.65029
X-RAY DIFFRACTIONf_chiral_restr0.047568
X-RAY DIFFRACTIONf_plane_restr0.004665
X-RAY DIFFRACTIONf_dihedral_angle_d14.6932145
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7439-1.78750.30561210.25142269239080
1.7875-1.83580.26451350.21622529266488
1.8358-1.88980.25871480.20662567271591
1.8898-1.95080.23891360.20262656279293
1.9508-2.02050.21231440.17732701284594
2.0205-2.10130.19431490.16592757290695
2.1013-2.19690.18851480.16322727287596
2.1969-2.31270.19321440.16752783292797
2.3127-2.45750.20351410.16162791293297
2.4575-2.6470.18871490.16082806295597
2.647-2.91310.19961510.16872806295798
2.9131-3.33380.20081490.16422846299599
3.3338-4.19740.17241560.14442884304099
4.1974-25.82140.16281440.15932939308399
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)
15.54870.1686-0.68143.98220.36784.06810.0872-0.8202-0.44710.33990.0301-0.08020.27430.0729-0.03270.186-0.002-0.05070.27620.05540.2087-13.9347.782663.2223
22.41680.43480.3892.81990.58521.8636-0.0522-0.0450.0781-0.19420.0715-0.151-0.20550.16190.00510.1347-0.03550.01760.1313-0.00230.1169-17.133818.270753.1683
34.4079-3.6643.24524.3365-3.17642.5566-0.1449-0.5298-0.23190.03590.29330.24210.0589-0.5053-0.14720.18710.0027-0.01850.20030.00890.2361-27.89762.171253.1324
47.62411.1156-2.09973.4058-0.40453.7859-0.16950.8856-0.4114-0.69460.1906-0.16870.1564-0.0140.01540.2805-0.04480.01790.2027-0.06520.1469-23.54864.660239.9933
52.46471.08-0.52512.30950.18752.1764-0.00270.0745-0.3715-0.26350.1213-0.24730.04020.1694-0.0810.16780.01050.00260.1219-0.0230.1951-20.6537-0.599248.0979
63.183-0.23580.21443.11660.02632.32130.0583-0.22970.31420.1336-0.1819-0.5141-0.24170.86870.07840.1624-0.0384-0.03390.38350.03340.2583-28.6638-9.195181.2101
72.3188-0.17851.25833.4357-0.06421.503-0.0203-0.2642-0.0321-0.1434-0.0315-0.30920.24340.39320.05470.11440.06160.0150.2250.02670.1548-35.1379-16.625978.2195
82.7814-0.32050.6462.8036-1.51322.76480.03820.2261-0.3033-0.5491-0.10390.08270.61910.274-0.02060.29990.07170.01650.14980.00010.1661-37.7393-23.124772.7627
92.1573-0.59750.65383.1963-1.36822.59720.16230.062-0.3871-0.4315-0.04350.29060.2938-0.0463-0.16740.2264-0.0105-0.0470.16230.00240.1772-45.2679-21.280974.1164
102.1570.0470.60962.8638-1.27142.46380.1008-0.2103-0.01180.09570.04660.34210.003-0.1386-0.07060.13650.00520.02060.1620.01380.1689-45.92-10.819980.2647
112.39672.75722.6144.81651.99833.47930.02240.59090.0247-0.13180.1221-0.10580.00630.4712-0.14070.17190.0034-0.0210.2430.00860.2136-40.4904-0.173467.5373
124.15240.8491-2.24573.8578-2.68774.2595-0.00470.0210.20260.19280.26280.699-0.6559-0.7839-0.17260.17580.0406-0.01230.18560.03920.2524-53.4269-3.451573.0531
135.7434-0.8351-2.99742.84490.9724.2168-0.0753-0.59490.12740.42740.01580.1232-0.34140.26690.04730.23740.00570.00410.148-0.01630.1559-42.3653-1.122682.7546
143.6706-0.68760.12462.86371.77869.5462-0.10720.08130.0202-0.08560.00670.01090.1766-0.2179-0.01470.1341-0.0148-0.01660.08910.00150.1489-46.83314.819469.0847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 76 )A32 - 76
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 199 )A77 - 199
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 215 )A200 - 215
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 229 )A216 - 229
5X-RAY DIFFRACTION5chain 'A' and (resid 230 through 262 )A230 - 262
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 102 )B32 - 102
7X-RAY DIFFRACTION7chain 'B' and (resid 103 through 122 )B103 - 122
8X-RAY DIFFRACTION8chain 'B' and (resid 123 through 146 )B123 - 146
9X-RAY DIFFRACTION9chain 'B' and (resid 147 through 163 )B147 - 163
10X-RAY DIFFRACTION10chain 'B' and (resid 164 through 199 )B164 - 199
11X-RAY DIFFRACTION11chain 'B' and (resid 200 through 215 )B200 - 215
12X-RAY DIFFRACTION12chain 'B' and (resid 216 through 229 )B216 - 229
13X-RAY DIFFRACTION13chain 'B' and (resid 230 through 245 )B230 - 245
14X-RAY DIFFRACTION14chain 'B' and (resid 246 through 263 )B246 - 263

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