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- PDB-5acx: VIM-2-2, Discovery of novel inhibitor scaffolds against the metal... -

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Basic information

Entry
Database: PDB / ID: 5acx
TitleVIM-2-2, Discovery of novel inhibitor scaffolds against the metallo- beta-lactamase VIM-2 by SPR based fragment screening
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE
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 / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HYDROXIDE ION / 2-(4-fluorophenyl)carbonylbenzoic acid / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChristopeit, T. / Carlsen, T.J.O. / Helland, R. / Leiros, H.K.S.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Discovery of Novel Inhibitor Scaffolds Against the Metallo-Beta-Lactamase Vim-2 by Spr Based Fragment Screening
Authors: Christopeit, T. / Carlsen, T.J.O. / Helland, R. / Leiros, H.K.S.
History
DepositionAug 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Jun 27, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-LACTAMASE
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,85816
Polymers56,8022
Non-polymers1,05714
Water11,097616
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-4.6 kcal/mol
Surface area22150 Å2
MethodPQS
Unit cell
Length a, b, c (Å)101.230, 79.220, 67.640
Angle α, β, γ (deg.)90.00, 130.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2008-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BETA-LACTAMASE /


Mass: 28400.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: 301-5473 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K2N0, beta-lactamase

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Non-polymers , 5 types, 630 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-WL3 / 2-(4-fluorophenyl)carbonylbenzoic acid


Mass: 244.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H9FO3
#4: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 1.82 Å3/Da / Density % sol: 32.57 % / Description: NONE
Crystal growpH: 7.2
Details: 22-27% PEG 3350, 0.2 M MAGNESIUM FORMATE, 5 MM BETA-MERCAPTOETHANOL, pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→39.61 Å / Num. obs: 37525 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 16.97 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.1
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.6 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KO3

1ko3


Resolution: 1.8→39.61 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 1805 4.8 %
Rwork0.1451 --
obs0.1474 37525 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 48 616 4176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043827
X-RAY DIFFRACTIONf_angle_d0.8925261
X-RAY DIFFRACTIONf_dihedral_angle_d13.5391376
X-RAY DIFFRACTIONf_chiral_restr0.032587
X-RAY DIFFRACTIONf_plane_restr0.004704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84870.22041400.18442737X-RAY DIFFRACTION99
1.8487-1.90310.2181250.18592739X-RAY DIFFRACTION99
1.9031-1.96450.26051200.20632697X-RAY DIFFRACTION97
1.9645-2.03470.25561150.16292778X-RAY DIFFRACTION99
2.0347-2.11620.17411540.15432717X-RAY DIFFRACTION99
2.1162-2.21250.19911400.15322751X-RAY DIFFRACTION99
2.2125-2.32910.22031370.15792693X-RAY DIFFRACTION98
2.3291-2.4750.19511640.13632732X-RAY DIFFRACTION100
2.475-2.66610.18791790.1422713X-RAY DIFFRACTION100
2.6661-2.93430.19881440.13932760X-RAY DIFFRACTION100
2.9343-3.35870.16991540.13182763X-RAY DIFFRACTION100
3.3587-4.23080.18961160.12432793X-RAY DIFFRACTION99
4.2308-39.61960.1621170.13812847X-RAY DIFFRACTION99
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)
13.5588-0.2416-0.33133.7211-0.18362.80090.1551-0.5559-0.32150.4448-0.01370.10310.6313-0.13220.06220.319-0.0553-0.04650.24190.0420.1645-20.45386.669111.9499
22.09830.20551.15311.0940.34922.59370.0629-0.13210.04230.0307-0.0265-0.0358-0.0374-0.0411-0.01840.1221-0.02350.01680.0789-0.00120.113-23.922319.34333.0824
32.55430.04630.77381.6399-0.06051.50.09340.0247-0.1184-0.0413-0.0119-0.03650.16170.0406-0.06470.12520.0046-0.00720.0684-0.01580.1044-27.11774.3309-3.5726
47.85580.31391.11361.9568-0.1262.39220.0041-0.0112-0.22230.01680.02130.05120.354-0.0733-0.02090.2101-0.0135-0.02760.07490.00120.1688-32.6131-4.3557-4.7377
50.88330.05351.16293.75770.91341.9944-0.0257-0.28870.6663-0.0371-0.0327-0.1267-0.44630.6279-0.00820.1981-0.0413-0.05870.275-0.05480.3686-33.4019-3.37831.9169
62.32960.0556-1.38094.3805-0.73657.6937-0.10770.43670.5606-0.6466-0.105-0.2475-0.35630.47910.17340.1727-0.0219-0.02760.31380.07820.251-35.3177-7.057323.768
73.79431.0372-1.38023.9653-0.02843.3372-0.04750.01490.12540.0442-0.0548-0.08480.15130.54570.12340.07080.0189-0.02140.15270.01780.1459-39.7162-13.016530.7259
81.4241-1.0058-0.7143.3451.8295.8201-0.01210.10520.44510.13250.2441-0.41550.0430.5533-0.19750.11310.0241-0.02190.31240.02190.2855-30.1117-14.56732.4164
92.8394-1.02372.23871.6910.12373.71510.03450.21250.18810.0028-0.1365-0.09630.08870.40490.0790.11610.03050.01330.13760.03650.1556-41.1675-17.066626.1935
103.0181-0.81910.72891.8278-0.09982.50340.04770.363-0.2448-0.11-0.05430.09680.34230.2215-0.00950.16640.0285-0.0050.1286-0.01470.1351-46.7184-22.946121.7611
110.8448-0.51121.34851.3672-0.03084.13850.0276-0.070.02180.0581-0.02220.11130.0369-0.0553-0.00760.0842-0.00680.01880.115-0.00030.1397-52.3241-11.645628.5542
120.77081.18311.92445.22152.71335.6674-0.15580.31140.1626-0.38640.0611-0.2683-0.57810.67090.04740.1689-0.00870.00010.22920.05040.2052-46.7396-0.721316.4366
133.6074-0.3065-0.84773.0551-1.046.1746-0.0341-0.11660.06260.0543-0.07720.3646-0.2204-0.61710.00970.09210.0235-0.03060.1109-0.01740.1789-59.3396-4.193321.8007
144.9597-0.1571-0.82273.03930.4834.6635-0.0512-0.22310.33840.2562-0.0255-0.0682-0.37420.16390.02090.14640.0142-0.03580.0922-0.01740.1261-48.5827-1.847731.5358
154.5994-1.00111.65315.7582-0.50825.2423-0.20980.20950.2421-0.1502-0.0809-0.0454-0.3787-0.17680.19710.12340.0231-0.01150.0741-0.00590.184-53.49973.941717.3732
16-0000-000-0-0-87057.19-177834.7-1655026.5877204621.611329616.2177834.78840.20560.07070.020.26570.05370.3388-44.6895-10.010216.6372
1700-00000-043468.534000-43468.540-00.4751-0.072-0.03640.28570.05010.3244-42.8672-7.763218.9425
180000-00-0000-0-32170.188-032170.1800.34850.0016-0.10730.13860.00950.2779-44.1669-31.003230.4424
19000000-01382.2774-048719.0155805.896-1041866.6329-127237.4972915.34-55805.89590.349-0.0583-0.02490.197-0.01970.2088-34.025910.2723.3519
200000-00-0-0-0-51961.48103302.91791154.831478996.346-358845-103302.91410.3488-0.0662-0.05620.27690.06840.47-31.52638.16045.0781
21000000-0320.6389-0-320.63890-10260.4447-010260.444-00.2018-0.0197-0.02720.12880.0050.2442-20.398230.92190.8714
220-000-00212975.77-32222.53-1602617.3831-912.6373-391.0296-285.3245644260.04-33803.04-212584.74380.2267-0.1433-0.23440.16070.05220.747-18.316730.53940.5364
2300-0000-9595.016-877.74712312.94320-00-110934.112288.3219595.01690.4894-0.0547-0.0466-0.11820.0250.2928-20.873230.30912.9513
240-000-00-80679.09-39536.451062662.4064-11469.9-2657.709-2569.7611-131594370563.45583336.80460.5161-0.0423-0.10330.1751-0.07060.4771-41.9263-30.589630.1234
2500-0000-22612.62-40001.97-41966.3580-00-18782923268.60222612.62310.7041-0.0916-0.1274-0.0212-0.15760.1601-44.6371-30.512432.5486
264.13241.0599-0.75651.83930.83643.80020.1267-0.1228-0.02730.02290.1101-0.53060.45220.5468-0.18560.41790.0775-0.02940.4909-0.0780.499-41.1258-7.509715.5729
271.0375-0.9604-0.11073.45610.04941.2930.1092-0.14490.16390.29240.01710.0115-0.04210.2908-0.05160.42240.0524-0.08450.8048-0.05010.5368-34.74388.1257.0617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 29 THROUGH 76 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 77 THROUGH 190 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 191 THROUGH 279 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 280 THROUGH 296 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 29 THROUGH 51 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 52 THROUGH 64 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 66 THROUGH 88 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 89 THROUGH 103 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 104 THROUGH 124 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 125 THROUGH 180 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 181 THROUGH 222 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 223 THROUGH 238 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 239 THROUGH 252 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 253 THROUGH 279 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 280 THROUGH 297 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 1 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 2 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 3 )
19X-RAY DIFFRACTION19CHAIN 'A' AND (RESID 1 )
20X-RAY DIFFRACTION20CHAIN 'A' AND (RESID 2 )
21X-RAY DIFFRACTION21CHAIN 'A' AND (RESID 3 )
22X-RAY DIFFRACTION22CHAIN 'A' AND (RESID 1300 )
23X-RAY DIFFRACTION23CHAIN 'A' AND (RESID 1301 )
24X-RAY DIFFRACTION24CHAIN 'B' AND (RESID 1300 )
25X-RAY DIFFRACTION25CHAIN 'B' AND (RESID 1301 )
26X-RAY DIFFRACTION26CHAIN 'A' AND (RESID 1298 )
27X-RAY DIFFRACTION27CHAIN 'B' AND (RESID 1298 )

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