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- PDB-7afx: Crystal structure of the metallo-beta-lactamase VIM2 with 139 -

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Basic information

Entry
Database: PDB / ID: 7afx
TitleCrystal structure of the metallo-beta-lactamase VIM2 with 139
ComponentsBeta-lactamase VIM-2
KeywordsANTIBIOTIC / HYDROLASE / HYDROLASES / MBL / 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
FORMIC ACID / Chem-R9K / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.636 Å
AuthorsBrem, J. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Innovative Medicines InitiativeEnable United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the metallo-beta-lactamase VIM2 with 139
Authors: Brem, J. / Schofield, C.J.
History
DepositionSep 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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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)52,62716
Polymers51,3872
Non-polymers1,24014
Water6,395355
1
A: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3148
Polymers25,6931
Non-polymers6207
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3148
Polymers25,6931
Non-polymers6207
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.251, 79.066, 67.951
Angle α, β, γ (deg.)90.000, 130.370, 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
Production host: Escherichia coli (E. coli) / Strain (production host): pLysS / References: UniProt: Q9K2N0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-R9K / 3-(2-chlorophenyl)-7-methyl-1~{H}-indole-2-carboxylic acid


Mass: 285.725 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12ClNO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.82 %
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 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 1.63→29.14 Å / Num. obs: 49690 / % possible obs: 96.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.14 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.065 / Rrim(I) all: 0.122 / Net I/σ(I): 9.3 / Num. measured all: 168749
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.63-1.673.30.7121022430710.6960.4520.8471.980.2
7.3-29.143.50.03319795640.9980.0210.03931.293.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.02 Å29.14 Å
Translation6.02 Å29.14 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ3
Resolution: 1.636→29.139 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1812 1993 4.01 %
Rwork0.1605 47649 -
obs0.1614 49642 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.47 Å2 / Biso mean: 20.1999 Å2 / Biso min: 7.93 Å2
Refinement stepCycle: final / Resolution: 1.636→29.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3451 0 96 378 3925
Biso mean--17.94 28.97 -
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043686
X-RAY DIFFRACTIONf_angle_d0.7195061
X-RAY DIFFRACTIONf_chiral_restr0.049574
X-RAY DIFFRACTIONf_plane_restr0.005668
X-RAY DIFFRACTIONf_dihedral_angle_d9.8862141
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6365-1.67740.29771320.26314690
1.6774-1.72280.24481480.2317346799
1.7228-1.77340.24981410.2092346699
1.7734-1.83070.2081440.1964343598
1.8307-1.89610.22251410.1865342498
1.8961-1.9720.21831410.181343697
1.972-2.06170.20561370.1589325594
2.0617-2.17040.17481520.1466345498
2.1704-2.30630.19551400.145348799
2.3063-2.48430.16041490.1404347299
2.4843-2.73410.1511460.1413346398
2.7341-3.12940.17221460.1443344698
3.1294-3.94110.1441370.1369326693
3.9411-29.10.16841390.1647343295
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.6573-0.25830.61021.6126-0.52711.8115-0.03430.03730.083-0.06760.01890.0607-0.0153-0.0929-0.00860.1133-0.00030.0030.10040.00540.1013-41.340922.692172.2345
23.5636-0.39861.17921.8953-0.85643.0085-0.0249-0.01560.20520.0548-0.0061-0.0934-0.15320.07930.07390.1405-0.0092-0.00090.1003-0.0150.1235-36.036429.01674.8212
30.8073-0.0940.28062.5458-2.34252.43190.0474-0.11630.10750.4160.0082-0.0724-0.56230.1032-0.0660.2011-0.00750.00050.1402-0.01850.1397-36.566826.61382.766
41.34840.1480.73611.7131-0.42731.27320.0003-0.1242-0.08170.09670.01170.0466-0.0545-0.0518-0.00160.1148-0.00580.02410.10150.0040.0971-38.739713.330380.8569
59.818-0.6673-2.90061.84510.27813.6646-0.0694-0.5553-0.26050.19520.05920.07330.0472-0.10020.06740.1317-0.0043-0.01210.14970.02540.107-34.60579.14289.1196
62.3127-0.2564-1.35791.76120.12855.54880.069-0.0386-0.06430.07780.04120.31760.2467-0.3679-0.09110.1213-0.01530.01130.13310.01830.1586-45.41577.107179.6762
76.7817-0.75920.49861.56520.22291.4495-0.015-0.1312-0.14360.08620.0070.05230.0818-0.00090.01820.15660.0027-0.0040.11660.01390.1201-30.94531.549882.377
83.85760.5882-1.48282.35141.37492.6859-0.21510.15720.65280.03210.12510.7349-0.6081-0.69560.05690.25970.0837-0.05210.28990.01580.3153-33.92953.72250.0792
92.2429-0.52-0.70152.65630.82933.1713-0.12030.1324-0.0357-0.1407-0.03710.15360.1233-0.1280.12970.1099-0.0041-0.02010.10730.00620.1218-26.7435-4.322547.5741
102.75290.30190.31143.4236-1.58.7596-0.03560.03250.1805-0.2942-0.0190.5162-0.0603-0.75070.06160.13180.0045-0.05970.1811-0.03320.2125-34.9018-9.215245.6805
111.64550.41881.26241.39480.6152.6843-0.00440.0924-0.01160.0003-0.00080.09760.0791-0.0190.01830.1311-0.01330.010.0971-00.1276-23.6778-11.390950.8703
123.50850.52751.06981.60121.00493.63650.0604-0.1849-0.1220.2417-0.02660.03070.2875-0.038-0.05980.20040.00030.01150.09590.00360.1536-21.3869-17.836756.6955
130.8330.19270.25821.79630.27410.82790.0020.0334-0.0387-0.0330.0149-0.05630.01590.0873-0.00380.11030.00140.01290.1288-0.00330.1131-14.2235-5.474553.7373
143.6-0.3849-2.4352.76170.95071.96420.0221-0.11380.0527-0.11150.0649-0.3193-0.10790.257-0.04850.1027-0.01160.00170.1377-0.00710.1155-5.44791.242156.3322
155.8737-0.4596-2.40481.58890.81732.72970.03740.30220.3336-0.4042-0.0153-0.0287-0.2050.0236-0.01960.1686-0.0167-0.00830.11370.02440.1074-16.09443.624846.5835
162.20120.14620.78132.00030.35017.5391-0.0729-0.02790.1603-0.03420.0426-0.0015-0.22690.16450.03470.1151-0.00810.00260.1096-0.01480.1575-11.50699.489859.906
173.54630.8011-0.41782.0843-0.39310.9579-0.01290.6844-0.553-0.3503-0.0350.06350.2475-0.32160.02550.2283-0.0119-0.03880.2622-0.06360.2467-47.60359.252364.3225
184.3567-1.3716-1.56282.41340.73952.04220.13080.00530.1247-0.1604-0.0083-0.0403-0.12480.0684-0.10060.1320.0038-0.00880.1261-0.00330.1277-42.218814.161867.8542
192.96730.2749-0.50751.4168-0.27772.1070.0523-0.03780.20580.00610.0290.0852-0.0826-0.0185-0.09850.12390.00020.00120.1284-0.00070.1619-46.178421.857971.4215
201.37830.9899-1.02512.8562-0.44343.6903-0.11710.36660.1132-0.55820.14560.40360.2825-0.3568-0.02760.16450.0045-0.04970.16120.01270.1534-48.215121.534761.8161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 103 through 122 )B103 - 122
2X-RAY DIFFRACTION2chain 'B' and (resid 123 through 146 )B123 - 146
3X-RAY DIFFRACTION3chain 'B' and (resid 147 through 163 )B147 - 163
4X-RAY DIFFRACTION4chain 'B' and (resid 164 through 215 )B164 - 215
5X-RAY DIFFRACTION5chain 'B' and (resid 216 through 229 )B216 - 229
6X-RAY DIFFRACTION6chain 'B' and (resid 230 through 245 )B230 - 245
7X-RAY DIFFRACTION7chain 'B' and (resid 246 through 263 )B246 - 263
8X-RAY DIFFRACTION8chain 'A' and (resid 32 through 44 )A32 - 44
9X-RAY DIFFRACTION9chain 'A' and (resid 45 through 88 )A45 - 88
10X-RAY DIFFRACTION10chain 'A' and (resid 89 through 102 )A89 - 102
11X-RAY DIFFRACTION11chain 'A' and (resid 103 through 122 )A103 - 122
12X-RAY DIFFRACTION12chain 'A' and (resid 123 through 146 )A123 - 146
13X-RAY DIFFRACTION13chain 'A' and (resid 147 through 215 )A147 - 215
14X-RAY DIFFRACTION14chain 'A' and (resid 216 through 229 )A216 - 229
15X-RAY DIFFRACTION15chain 'A' and (resid 230 through 245 )A230 - 245
16X-RAY DIFFRACTION16chain 'A' and (resid 246 through 263 )A246 - 263
17X-RAY DIFFRACTION17chain 'B' and (resid 31 through 52 )B31 - 52
18X-RAY DIFFRACTION18chain 'B' and (resid 53 through 76 )B53 - 76
19X-RAY DIFFRACTION19chain 'B' and (resid 77 through 88 )B77 - 88
20X-RAY DIFFRACTION20chain 'B' and (resid 89 through 102 )B89 - 102

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