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- PDB-5ewa: Crystal structure of the metallo-beta-lactamase IMP-1 in complex ... -

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Basic information

Entry
Database: PDB / ID: 5ewa
TitleCrystal structure of the metallo-beta-lactamase IMP-1 in complex with the bisthiazolidine inhibitor L-VC26
ComponentsBeta-lactamase IMP-1
KeywordsHYDROLASE / inhibitor / carbapenemase / antibiotic resistance
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / 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 ...Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / 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
Chem-9BZ / Metallo-beta-lactamase IMP-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKosmopoulou, M. / Hinchliffe, P. / Spencer, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Cross-class metallo-beta-lactamase inhibition by bisthiazolidines reveals multiple binding modes.
Authors: Hinchliffe, P. / Gonzalez, M.M. / Mojica, M.F. / Gonzalez, J.M. / Castillo, V. / Saiz, C. / Kosmopoulou, M. / Tooke, C.L. / Llarrull, L.I. / Mahler, G. / Bonomo, R.A. / Vila, A.J. / Spencer, J.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase IMP-1
B: Beta-lactamase IMP-1
C: Beta-lactamase IMP-1
D: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,92918
Polymers101,2034
Non-polymers1,72514
Water5,513306
1
A: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7595
Polymers25,3011
Non-polymers4584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6974
Polymers25,3011
Non-polymers3963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7755
Polymers25,3011
Non-polymers4744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6974
Polymers25,3011
Non-polymers3963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.054, 78.448, 260.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase IMP-1 / BLAIMP / Beta-lactamase type II / Penicillinase. Metallo-beta-lactamase class B1 IMP-1


Mass: 25300.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Plasmid: pOPIN-F / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): solu / References: UniProt: P52699, beta-lactamase

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Non-polymers , 5 types, 320 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-9BZ / (3~{R},5~{R},7~{a}~{S})-2,2-dimethyl-5-(sulfanylmethyl)-3,5,7,7~{a}-tetrahydro-[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid / L-VC26


Mass: 265.416 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15NO2S3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 6.0, 0.2 M sodium acetate, 25% PEG 8000. 1ul protein (25 mg/ml) mixed with 1ul reagent

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→29.82 Å / Num. obs: 45814 / % possible obs: 99.9 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 18.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.521 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DDK

1ddk


Resolution: 2.3→29.82 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 2323 5.07 %
Rwork0.182 --
obs0.184 45787 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6870 0 76 306 7252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087117
X-RAY DIFFRACTIONf_angle_d1.1769668
X-RAY DIFFRACTIONf_dihedral_angle_d14.1572596
X-RAY DIFFRACTIONf_chiral_restr0.0611075
X-RAY DIFFRACTIONf_plane_restr0.0061204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.34690.2691510.23762511X-RAY DIFFRACTION100
2.3469-2.39790.2611240.23442484X-RAY DIFFRACTION100
2.3979-2.45370.25521390.21792578X-RAY DIFFRACTION100
2.4537-2.5150.27561310.22272461X-RAY DIFFRACTION100
2.515-2.5830.31511240.22582566X-RAY DIFFRACTION100
2.583-2.6590.2531390.22352478X-RAY DIFFRACTION100
2.659-2.74470.28961240.2082540X-RAY DIFFRACTION100
2.7447-2.84270.25051450.20932505X-RAY DIFFRACTION100
2.8427-2.95650.25851390.20582529X-RAY DIFFRACTION100
2.9565-3.09090.27311410.19772560X-RAY DIFFRACTION100
3.0909-3.25370.24511220.1942562X-RAY DIFFRACTION100
3.2537-3.45720.22421240.18242552X-RAY DIFFRACTION100
3.4572-3.72370.18961520.17552566X-RAY DIFFRACTION100
3.7237-4.09760.2021340.15882583X-RAY DIFFRACTION100
4.0976-4.68850.15971470.14152579X-RAY DIFFRACTION100
4.6885-5.89960.19321450.14812627X-RAY DIFFRACTION100
5.8996-29.82410.19631420.1622783X-RAY DIFFRACTION100
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)
17.52011.93513.28953.16012.24956.3822-0.04060.6111-0.2822-0.3740.2304-0.066-0.0402-0.0654-0.19120.48070.05590.03310.24260.03920.188617.8236-9.3426-42.6752
24.80361.53172.72374.4391.84867.07420.20910.6066-0.3676-0.1849-0.0174-0.41860.10050.5358-0.14480.20060.04480.05840.1501-0.01160.2219.7099-8.4108-34.1164
37.84983.09692.94233.48912.43.645-0.13540.6469-0.62950.05360.1317-0.21970.0660.3354-0.06780.32280.03970.00680.2001-0.03390.259423.595-17.6661-35.7872
49.4216-2.5327-2.26254.18722.42282.3676-0.00890.1208-0.0285-0.0191-0.0669-0.31540.06010.20530.06860.26410.0161-0.01650.16540.06760.203717.1119-10.4592-30.1071
56.9812-0.9331-0.22313.11661.28435.5969-0.11-0.361-0.16740.1249-0.00950.18070.0606-0.04720.14430.22170.00240.02910.13130.04270.118211.4273-10.0641-22.6652
62.7903-0.8421-0.78022.65-0.27184.39310.07740.36290.4113-0.1412-0.0556-0.0894-0.7797-0.1956-0.00760.37460.0478-0.00960.16190.02880.24312.23412.7259-31.756
73.6703-1.27270.01264.7366-0.03743.16890.07260.37490.7115-0.1817-0.0837-0.0319-1.257-0.44330.02450.68520.1566-0.03160.32220.09660.34028.51519.4234-37.4734
89.07133.44740.79724.5212-0.04344.32640.491-0.5839-0.19570.3942-0.4276-0.1402-0.18090.1857-0.06680.45650.04-0.02910.274-0.01560.142913.0906-11.202411.6613
91.02841.594-0.75083.9030.372.26310.0221-0.17740.2980.3545-0.0760.0999-0.2398-0.04870.07520.21640.0298-0.02080.1467-0.00830.14889.4259-10.26463.58
105.44283.6363-0.50465.9041-1.21012.54230.0031-0.165-0.13120.3196-0.1133-0.1154-0.19940.16180.10940.14220.0312-0.03360.1679-0.01520.12811.0455-14.86211.0372
114.27531.70720.18726.7460.11694.3773-0.11310.28390.340.01910.0916-0.1397-0.4150.21740.04190.2226-0.0487-0.05630.1870.01690.134615.3171-6.9239-8.9731
121.55120.9856-0.25394.4950.76523.1391-0.2561-0.31150.64560.63810.14490.1311-1.085-0.15050.10910.71060.0879-0.12470.2261-0.07060.416612.26396.59335.7037
137.62045.85052.48239.38992.69364.57690.3187-0.4158-0.07781.6172-0.384-0.22010.59310.05760.00850.69070.0560.00890.33110.0390.29916.5769-40.8244-21.7007
141.959-0.0644-0.76772.2950.8914.2982-0.12470.0087-0.19410.3038-0.1130.07810.7003-0.36950.2160.2659-0.0670.02870.1734-0.03620.20990.0155-36.9626-33.4709
157.982.0356-0.28045.9736-1.34164.1255-0.2346-0.7586-0.33370.8240.60890.0090.3233-1.1983-0.39730.3949-0.10360.00870.99210.05260.2542-4.0463-5.43-53.1406
165.82264.429-0.79083.4281-1.18627.9802-0.1141-0.51770.27120.27650.08630.6391-0.4201-0.9754-0.00650.17030.05610.00670.64710.01590.2995-4.6565-0.6497-60.8034
175.5477-0.8073-1.96221.72330.16051.9591-0.1655-0.53050.25690.23580.13810.2796-0.1395-1.39610.03910.30950.1035-0.00511.03290.01150.2829-9.2742-2.3773-63.1242
184.4754-0.86320.54372.15010.70914.00960.08380.60320.2981-0.3137-0.27390.0598-0.1807-0.28990.20740.25190.06530.03060.51690.10280.21440.5004-3.174-72.9898
193.2591-0.18120.41417.58272.30565.7906-0.1140.03420.09550.176-0.0082-0.16790.16630.51610.11290.18240.01490.03950.36960.08470.175512.5059-2.026-62.7375
207.0966-1.3765-0.44017.12762.47174.7057-0.0079-0.53990.20590.34120.0798-0.44990.36760.5826-0.06560.2020.0652-0.01620.55680.07430.238615.6655-3.5799-56.6478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 85 )
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 126 )
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 172 )
7X-RAY DIFFRACTION7chain 'A' and (resid 173 through 221 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 28 )
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 52 )
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 85 )
11X-RAY DIFFRACTION11chain 'B' and (resid 86 through 126 )
12X-RAY DIFFRACTION12chain 'B' and (resid 127 through 221 )
13X-RAY DIFFRACTION13chain 'C' and (resid 3 through 28 )
14X-RAY DIFFRACTION14chain 'C' and (resid 29 through 224 )
15X-RAY DIFFRACTION15chain 'D' and (resid 3 through 28 )
16X-RAY DIFFRACTION16chain 'D' and (resid 29 through 52 )
17X-RAY DIFFRACTION17chain 'D' and (resid 53 through 85 )
18X-RAY DIFFRACTION18chain 'D' and (resid 86 through 144 )
19X-RAY DIFFRACTION19chain 'D' and (resid 145 through 187 )
20X-RAY DIFFRACTION20chain 'D' and (resid 188 through 221 )

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