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- PDB-5lm6: VIM-2 metallo-beta-lactamase in complex with 2-(3-fluoro-4-hydrox... -

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Basic information

Entry
Database: PDB / ID: 5lm6
TitleVIM-2 metallo-beta-lactamase in complex with 2-(3-fluoro-4-hydroxyphenyl)-3-oxoisoindoline-4-carboxylic acid (compound 35)
ComponentsMetallo-beta-lactamase VIM-2
KeywordsHYDROLASE / metallo-beta-lactamase / inhibitor / complex / antibiotic resistance
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 / Chem-H32 / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.17 Å
AuthorsLi, G.-B. / Brem, J. / Someya, H. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Chem Sci / Year: 2017
Title: NMR-filtered virtual screening leads to non-metal chelating metallo-beta-lactamase inhibitors.
Authors: Li, G.B. / Abboud, M.I. / Brem, J. / Someya, H. / Lohans, C.T. / Yang, S.Y. / Spencer, J. / Wareham, D.W. / McDonough, M.A. / Schofield, C.J.
History
DepositionJul 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jan 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.ptnr2_symmetry / _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_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
B: Metallo-beta-lactamase VIM-2
A: Metallo-beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,56913
Polymers56,7062
Non-polymers86411
Water8,575476
1
B: Metallo-beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6416
Polymers28,3531
Non-polymers2885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Metallo-beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9287
Polymers28,3531
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.983, 80.251, 68.319
Angle α, β, γ (deg.)90.000, 130.000, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Metallo-beta-lactamase VIM-2 / Beta-lactamase VIM-2 / Class B beta-lactamase / Class B carbapenemase VIM-2 / Metallo beta ...Beta-lactamase VIM-2 / Class B beta-lactamase / Class B carbapenemase VIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase vim-2 / VIM-2 / VIM-2 beta-lactamase / VIM-2 protein


Mass: 28352.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 2-(3-fluoro-4-hydroxyphenyl)-3-oxoisoindoline-4-carboxylic acid
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 VECTOR BASED ON PTRIEX VECTOR / Details (production host): PLASMID DERIVED NON-GENOMIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-H32 / 2-(3-fluoranyl-4-oxidanyl-phenyl)-3-oxidanylidene-1~{H}-isoindole-4-carboxylic acid


Mass: 287.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C15H10FNO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Magnesium Formate, 21-26% (v/v) Polyethylene glycol 3350, 1 mM Tris(2-carboxyethyl)phosphine, 16 mg/mL protein; socked the crystals with 10mM 2-(3-fluoro-4-hydroxyphenyl)-3-oxoisoindoline-4-carboxylic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.17→52.01 Å / Num. obs: 142903 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 12.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Net I/σ(I): 8.8 / Num. measured all: 940952 / Scaling rejects: 498
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.17-1.26.51.2368542105490.6030.5171.3371.599.9
5.23-52.017.40.0571230216590.9960.0230.0623199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.32 Å24.9 Å
Translation6.32 Å24.9 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C1D

4c1d


Resolution: 1.17→52.01 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 7006 4.99 %
Rwork0.1902 133319 -
obs0.1912 140325 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.1 Å2 / Biso mean: 21.5922 Å2 / Biso min: 7.97 Å2
Refinement stepCycle: final / Resolution: 1.17→52.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 39 481 3968
Biso mean--23.9 32.97 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093786
X-RAY DIFFRACTIONf_angle_d15203
X-RAY DIFFRACTIONf_chiral_restr0.085582
X-RAY DIFFRACTIONf_plane_restr0.007693
X-RAY DIFFRACTIONf_dihedral_angle_d13.5031350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.17-1.18330.39852020.38854430463296
1.1833-1.19720.41672170.38124328454597
1.1972-1.21180.35162440.36594393463798
1.2118-1.22720.36712260.35974402462897
1.2272-1.24330.49541960.50054108430491
1.2433-1.26030.39932110.39294387459896
1.2603-1.27830.41022240.40664459468398
1.2783-1.29740.42862210.36354340456197
1.2974-1.31770.49482490.45494238448795
1.3177-1.33930.38532390.34494290452995
1.3393-1.36240.32082770.29434425470299
1.3624-1.38720.29562430.28774484472799
1.3872-1.41390.30152280.26994468469699
1.4139-1.44270.28062290.24984494472399
1.4427-1.47410.24962450.24544461470699
1.4741-1.50840.25892200.26494471469198
1.5084-1.54610.24472140.2284511472599
1.5461-1.58790.19742310.20064490472199
1.5879-1.63460.19922600.178844924752100
1.6346-1.68740.19212650.171844714736100
1.6874-1.74770.18262750.152144954770100
1.7477-1.81770.15232490.145345154764100
1.8177-1.90040.16172350.144545344769100
1.9004-2.00060.2431870.2124352453996
2.0006-2.1260.16932310.146645254756100
2.126-2.29010.20892350.17384501473699
2.2901-2.52060.16333010.14024459476099
2.5206-2.88530.15282190.135445574776100
2.8853-3.63510.15842110.137446044815100
3.6351-52.06180.16962220.14646354857100
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)
10.9054-1.65051.24219.4495-2.1652.0017-0.7529-0.05240.93030.81690.44080.639-0.9981-1.25390.18580.39650.155-0.11330.4703-0.050.379-34.66771.925250.4186
23.6711-0.29690.62983.5063-0.15613.0157-0.14870.01910.2951-0.12360.00930.1793-0.1265-0.44140.08930.07750.0031-0.03230.1494-0.01290.1139-26.9646-5.574347.4562
33.04970.8426-1.28035.2138-1.46394.3042-0.0721-0.07520.1918-0.28830.12910.45740.1683-0.8433-0.02030.0994-0.0241-0.04540.3151-0.0210.2006-35.1978-10.569845.9563
43.7360.89912.17122.23510.68124.1679-0.0706-0.01190.008-0.1063-0.05220.15730.021-0.1630.09650.0853-0.03480.01110.096-0.00980.097-23.729-12.470351.5321
54.01330.93470.57332.69950.84283.2880.1769-0.3563-0.37670.322-0.0662-0.0010.4585-0.2192-0.07510.1573-0.04260.01170.10850.02850.1423-20.8129-19.393357.5201
61.52080.46480.38531.97930.32541.67490.00870.0698-0.1296-0.05520.0064-0.14750.05540.0397-0.02380.0654-0.00010.00870.08780.00080.0874-12.7123-10.293651.6643
73.724-3.97214.1944.6295-5.31487.4624-0.1686-0.50980.09180.41830.26650.1801-0.2956-0.4525-0.14460.1531-0.00240.0020.1742-0.01940.1432-18.52414.03861.9318
83.4224-0.04480.24651.46570.28983.3882-0.08050.20230.1658-0.14030.0196-0.1318-0.25060.13370.05860.1002-0.01810.01240.04280.00880.0957-11.27491.605551.4549
95.6480.16240.77584.70820.37336.43550.0301-0.27340.23760.0430.0601-0.0494-0.00120.1889-0.06780.09420.0074-0.01140.0935-0.02190.1505-11.70748.615260.323
105.24121.34790.1273.1796-0.68292.2170.19640.9563-0.4889-0.4523-0.02070.02270.5675-0.0427-0.05250.23840.0319-0.06040.2833-0.06690.1901-45.213910.602765.3233
112.61381.41870.88912.3241-1.17812.07480.14760.4045-0.0815-0.048-0.09750.01220.12890.0515-0.19640.07760.0186-0.01990.1288-0.0140.0837-45.034414.599571.2881
124.914-0.2343-0.80723.52660.24984.3390.14740.21350.0038-0.1151-0.13440.3194-0.1974-0.178-0.05290.10440.0165-0.02280.10480.00720.1066-46.878721.537572.3463
138.8860.8685-0.45785.1374-0.76956.47550.09680.5301-0.0196-0.32620.04370.3810.2257-0.1582-0.10490.16720.0393-0.05180.19350.01070.1319-49.062121.363362.5085
147.3891-1.22152.97111.8631-1.17934.08960.19650.03160.0197-0.15-0.09630.09410.04010.0006-0.07130.11440.0046-0.00190.04930.01430.0767-41.568622.032573.3185
156.6841-1.86491.91952.0846-0.71173.4514-0.02890.1890.31650.0218-0.0599-0.0639-0.23850.25190.09490.142-0.0386-0.00020.07360.02460.0905-35.738728.876175.8192
161.7531-0.36460.47572.8896-1.25471.7338-0.01680.00330.13510.4213-0.0034-0.1407-0.4208-0.0080.08320.1899-0.0216-0.02370.1019-0.00770.1063-36.375826.505683.0309
172.3187-0.51060.15132.1309-0.48071.8077-0.0171-0.1523-0.02450.21240.01360.1834-0.1018-0.1307-0.00840.1007-0.00270.01890.0940.00320.0828-42.416615.995484.3227
187.61215.26923.90496.79324.372.9685-0.13620.5413-0.4677-0.28950.3129-0.4802-0.05320.4983-0.20490.14860.00710.01510.17860.01420.1529-30.75.498376.4093
193.46470.4093-0.04592.3649-0.31144.1253-0.0459-0.4829-0.21680.32170.020.0782-0.0160.1146-0.00180.1156-0.00790.00410.10.03840.0868-34.74898.211490.0818
203.51160.4262-0.2671.5279-0.06143.6840.04030.041-0.1860.0469-0.00090.290.2289-0.26670.00140.086-0.0150.01960.08690.0020.1497-45.81666.20280.0544
215.6658-1.3029-0.57963.08210.13764.65770.0074-0.1436-0.1470.0907-0.0393-0.08230.27060.29970.02740.14830.0077-0.01290.09030.01490.1127-31.46120.520583.1336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 44 )A32 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 88 )A45 - 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 199 )A147 - 199
7X-RAY DIFFRACTION7chain 'A' and (resid 200 through 215 )A200 - 215
8X-RAY DIFFRACTION8chain 'A' and (resid 216 through 245 )A216 - 245
9X-RAY DIFFRACTION9chain 'A' and (resid 246 through 262 )A246 - 262
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 64 )B32 - 64
11X-RAY DIFFRACTION11chain 'B' and (resid 65 through 76 )B65 - 76
12X-RAY DIFFRACTION12chain 'B' and (resid 77 through 88 )B77 - 88
13X-RAY DIFFRACTION13chain 'B' and (resid 89 through 102 )B89 - 102
14X-RAY DIFFRACTION14chain 'B' and (resid 103 through 122 )B103 - 122
15X-RAY DIFFRACTION15chain 'B' and (resid 123 through 146 )B123 - 146
16X-RAY DIFFRACTION16chain 'B' and (resid 147 through 162 )B147 - 162
17X-RAY DIFFRACTION17chain 'B' and (resid 163 through 199 )B163 - 199
18X-RAY DIFFRACTION18chain 'B' and (resid 200 through 215 )B200 - 215
19X-RAY DIFFRACTION19chain 'B' and (resid 216 through 229 )B216 - 229
20X-RAY DIFFRACTION20chain 'B' and (resid 230 through 245 )B230 - 245
21X-RAY DIFFRACTION21chain 'B' and (resid 246 through 262 )B246 - 262

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