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- PDB-5hh4: Crystal structure of metallo-beta-lactamase IMP-1 in complex with... -

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Basic information

Entry
Database: PDB / ID: 5hh4
TitleCrystal structure of metallo-beta-lactamase IMP-1 in complex with a phosphonate-based inhibitor
ComponentsBeta-lactamase IMP-1
KeywordsHYDROLASE / inhibitor / carbapenamase / pyridine / phosphonate / antibiotic resistance
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 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 / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
6-(phosphonomethyl)pyridine-2-carboxylic acid / Metallo-beta-lactamase IMP-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100135 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI100560 United States
CitationJournal: Biochemistry / Year: 2018
Title: Structural and Kinetic Studies of the Potent Inhibition of Metallo-beta-lactamases by 6-Phosphonomethylpyridine-2-carboxylates.
Authors: Hinchliffe, P. / Tanner, C.A. / Krismanich, A.P. / Labbe, G. / Goodfellow, V.J. / Marrone, L. / Desoky, A.Y. / Calvopina, K. / Whittle, E.E. / Zeng, F. / Avison, M.B. / Bols, N.C. / Siemann, ...Authors: Hinchliffe, P. / Tanner, C.A. / Krismanich, A.P. / Labbe, G. / Goodfellow, V.J. / Marrone, L. / Desoky, A.Y. / Calvopina, K. / Whittle, E.E. / Zeng, F. / Avison, M.B. / Bols, N.C. / Siemann, S. / Spencer, J. / Dmitrienko, G.I.
History
DepositionJan 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 27, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _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.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.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
Revision 1.4Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)102,32218
Polymers101,1434
Non-polymers1,17914
Water11,241624
1
A: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6344
Polymers25,2861
Non-polymers3483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7316
Polymers25,2861
Non-polymers4455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4794
Polymers25,2861
Non-polymers1933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4794
Polymers25,2861
Non-polymers1933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.943, 78.309, 260.545
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 / Class B1 Metallo-beta-lactamase IMP-1


Mass: 25285.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SoluBL21 / References: UniProt: P52699, beta-lactamase

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Non-polymers , 5 types, 638 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-60M / 6-(phosphonomethyl)pyridine-2-carboxylic acid


Mass: 217.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8NO5P
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
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: I02 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2→67.12 Å / Num. obs: 68602 / % possible obs: 99.7 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.191 / Net I/σ(I): 8.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8

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Processing

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

1ddk


Resolution: 2→58.158 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2057 3396 4.95 %
Rwork0.1716 --
obs0.1733 68593 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→58.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6864 0 49 624 7537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097092
X-RAY DIFFRACTIONf_angle_d1.1679623
X-RAY DIFFRACTIONf_dihedral_angle_d15.2532564
X-RAY DIFFRACTIONf_chiral_restr0.0531062
X-RAY DIFFRACTIONf_plane_restr0.0061206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02860.25261520.22682660X-RAY DIFFRACTION100
2.0286-2.05890.27861240.2222702X-RAY DIFFRACTION100
2.0589-2.0910.26851520.20732647X-RAY DIFFRACTION100
2.091-2.12530.25151320.20672724X-RAY DIFFRACTION100
2.1253-2.1620.2151350.19522646X-RAY DIFFRACTION100
2.162-2.20130.24271480.19782678X-RAY DIFFRACTION100
2.2013-2.24360.29371430.19532696X-RAY DIFFRACTION100
2.2436-2.28940.24561350.1862640X-RAY DIFFRACTION100
2.2894-2.33920.23011290.19152732X-RAY DIFFRACTION100
2.3392-2.39360.23781210.1822681X-RAY DIFFRACTION100
2.3936-2.45350.22141580.18072736X-RAY DIFFRACTION100
2.4535-2.51980.24831460.17832652X-RAY DIFFRACTION100
2.5198-2.5940.22741280.17132727X-RAY DIFFRACTION100
2.594-2.67770.20231630.1762685X-RAY DIFFRACTION100
2.6777-2.77340.24791430.17692710X-RAY DIFFRACTION100
2.7734-2.88440.21471450.18412756X-RAY DIFFRACTION100
2.8844-3.01570.24581300.18322712X-RAY DIFFRACTION100
3.0157-3.17470.2271480.17962711X-RAY DIFFRACTION100
3.1747-3.37360.21041560.17122704X-RAY DIFFRACTION99
3.3736-3.6340.1771470.16652741X-RAY DIFFRACTION100
3.634-3.99960.1771230.15472781X-RAY DIFFRACTION99
3.9996-4.57820.16491390.13722768X-RAY DIFFRACTION99
4.5782-5.76720.15051350.14282804X-RAY DIFFRACTION99
5.7672-58.18270.17831640.17012904X-RAY DIFFRACTION98
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)
12.71462.34430.72024.33851.3621.7409-0.0850.41740.058-0.42420.0624-0.0224-0.17210.20430.01220.3396-0.07070.09320.4398-0.06560.303222.1495-8.8575-42.5673
21.2673-0.2841-0.23252.2334-0.21372.0206-0.03180.2227-0.1186-0.35980.0178-0.03480.0456-0.12210.03670.22720.00380.00120.1848-0.01560.186615.8076-8.9943-37.162
32.8313-0.08110.16071.0943-0.01040.7772-0.15550.2808-0.295-0.24050.1579-0.18880.16040.1469-0.02330.16820.02480.02010.191-0.05290.234118.6511-13.5088-32.336
40.8272-0.12880.02681.1617-0.01831.3260.01570.077-0.003-0.0647-0.0484-0.0045-0.2169-0.05280.02050.17960.0188-0.01050.12520.01420.188310.7577-3.4908-27.2091
52.19880.1993-0.00821.68440.38011.1862-0.13310.25710.453-0.23240.0489-0.0825-0.4061-0.01990.03430.50260.068-0.05410.18240.08020.255810.6777.8457-35.5056
63.2265-0.2026-0.57261.7231-0.67481.4019-0.02020.31840.3024-0.24390.00160.2401-0.2661-0.2707-0.10240.65340.2174-0.13080.36710.17330.35812.678310.9801-41.1256
71.8799-0.72231.18341.2801-0.53341.5891-0.0592-0.31010.03740.3977-0.017-0.1527-0.00060.03170.07350.29720.037-0.01720.35550.01210.26328.9053-13.547613.3394
81.11010.32770.0971.55230.04121.34310.0286-0.1224-0.0240.2874-0.1050.0192-0.20110.20850.06280.17670.0065-0.02650.1980.00440.149311.3147-9.74576.3573
91.75530.8463-0.231.0969-0.44721.0054-0.0507-0.1446-0.08410.166-0.01810.0495-0.18210.01560.08510.06320.0215-0.00760.15720.02740.18329.9577-14.77310.9985
100.70480.1879-0.00361.1586-0.00161.3604-0.0315-0.11210.20550.18780.00380.1002-0.493-0.06080.02810.21360.0212-0.04630.1218-0.02540.247411.21840.6519-0.58
111.35170.5089-0.17741.69960.10421.0267-0.0944-0.16740.25930.2072-0.0519-0.0977-0.34670.0695-0.07690.8125-0.0317-0.07380.3423-0.26790.523415.637412.980512.3644
121.107-0.34750.22891.65250.55661.4497-0.027-0.2617-0.01380.2559-0.0297-0.04630.36120.09550.05850.51320.0205-0.04740.29710.03760.25284.5016-40.9715-21.5728
131.03-0.1482-0.27221.67240.12820.7082-0.0246-0.1359-0.13590.2418-0.0316-0.23840.58090.2460.03780.39170.0586-0.01180.2066-0.01580.24766.9877-44.3269-31.2534
141.2617-0.2882-0.34711.1270.18231.27940.0570.1284-0.0685-0.0487-0.08480.02920.3169-0.21430.01540.2131-0.0337-0.00940.1945-0.03750.1796-2.1742-35.3063-37.4909
151.9767-0.61-0.06332.7183-0.97681.4258-0.0577-0.00380.01570.1797-0.05440.22570.2426-0.36590.11160.2266-0.06440.03610.3079-0.0730.2072-11.4231-32.018-25.0645
160.88090.01480.32511.40830.65970.94660.1167-0.1603-0.07150.24170.0980.13440.0889-0.2614-0.12710.5966-0.1766-0.05451.3660.02880.3194-5.80091.2217-52.0884
171.1984-0.10270.70481.94010.11031.91990.2965-0.137-0.31930.0765-0.19010.02840.38680.074-0.13770.4824-0.2763-0.17021.13620.12580.3062-1.9458-8.4839-55.1632
180.34030.10340.10840.62550.04781.52530.0764-0.1754-0.07430.0279-0.14790.1598-0.0814-0.57-0.12250.4822-0.2495-0.07261.36010.13480.0532-7.88380.5075-60.7514
191.3010.17120.42650.74330.01041.21980.2402-0.2182-0.1343-0.0443-0.2108-0.01240.1944-0.54680.00840.4102-0.053-0.03230.70770.12710.25412.3695-1.9739-68.6213
202.1232-0.5222-0.64241.52960.4272.1936-0.0537-0.05390.00770.0802-0.0761-0.37450.03150.32570.1090.2919-0.1215-0.00990.64530.1270.338516.5353-2.3911-58.9245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 172 )
5X-RAY DIFFRACTION5chain 'A' and (resid 173 through 202 )
6X-RAY DIFFRACTION6chain 'A' and (resid 203 through 220 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 15 )
8X-RAY DIFFRACTION8chain 'B' and (resid 16 through 52 )
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 85 )
10X-RAY DIFFRACTION10chain 'B' and (resid 86 through 202 )
11X-RAY DIFFRACTION11chain 'B' and (resid 203 through 220 )
12X-RAY DIFFRACTION12chain 'C' and (resid 4 through 28 )
13X-RAY DIFFRACTION13chain 'C' and (resid 29 through 85 )
14X-RAY DIFFRACTION14chain 'C' and (resid 86 through 187 )
15X-RAY DIFFRACTION15chain 'C' and (resid 188 through 219 )
16X-RAY DIFFRACTION16chain 'D' and (resid 3 through 15 )
17X-RAY DIFFRACTION17chain 'D' and (resid 16 through 28 )
18X-RAY DIFFRACTION18chain 'D' and (resid 29 through 65 )
19X-RAY DIFFRACTION19chain 'D' and (resid 66 through 172 )
20X-RAY DIFFRACTION20chain 'D' and (resid 173 through 219 )

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