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- PDB-5hh6: Crystal structure of B3 metallo-beta-lactamase L1 in complex with... -

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Basic information

Entry
Database: PDB / ID: 5hh6
TitleCrystal structure of B3 metallo-beta-lactamase L1 in complex with a phosphonate-based inhibitor
ComponentsMetallo-beta-lactamase L1
KeywordsHYDROLASE / inhibitor / carbapenamase / pyridine / phosphonate / antibiotic resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-60N / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.1Feb 1, 2017Group: Structure summary
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author / 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 1.4Apr 14, 2021Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_ISSN / _pdbx_struct_assembly.details ..._citation.journal_id_ISSN / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.5Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / pdbx_struct_oper_list
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_oper_list.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.6Jan 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: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3855
Polymers28,8951
Non-polymers4914
Water4,720262
1
A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,54120
Polymers115,5784
Non-polymers1,96316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Unit cell
Length a, b, c (Å)105.347, 105.347, 98.835
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

21A-736-

HOH

31A-740-

HOH

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Components

#1: Protein Metallo-beta-lactamase L1 / Class B3 metallo-beta-lactamase L1 / Beta-lactamase type II / Penicillinase


Mass: 28894.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SoluBL21 / References: UniProt: P52700, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-60N / 6-[(~{S})-oxidanyl(phosphono)methyl]pyridine-2-carboxylic acid


Mass: 233.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8NO6P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM Hepes pH 7.75, 2.0 M ammonium sulphate, 1.5% PEG400. 1 ul protein (15 mg/ml) mixed with 1 ul reservoir.

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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: 1.8→46.48 Å / Num. obs: 30533 / % possible obs: 100 % / Redundancy: 38.9 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 25.9
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 40.4 % / Rmerge(I) obs: 1.419 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

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

1sml


Resolution: 1.8→46.48 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1879 1527 5 %
Rwork0.1581 --
obs0.1595 30533 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 26 262 2289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072082
X-RAY DIFFRACTIONf_angle_d1.0392846
X-RAY DIFFRACTIONf_dihedral_angle_d14.115738
X-RAY DIFFRACTIONf_chiral_restr0.046314
X-RAY DIFFRACTIONf_plane_restr0.006374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85810.24561390.21622569X-RAY DIFFRACTION100
1.8581-1.92460.23651380.19282583X-RAY DIFFRACTION100
1.9246-2.00160.21431240.17912595X-RAY DIFFRACTION100
2.0016-2.09270.21261310.17292597X-RAY DIFFRACTION100
2.0927-2.2030.23711350.16252609X-RAY DIFFRACTION100
2.203-2.34110.18681260.162627X-RAY DIFFRACTION100
2.3411-2.52180.1981390.16012604X-RAY DIFFRACTION100
2.5218-2.77560.18341460.16282637X-RAY DIFFRACTION100
2.7756-3.17710.18961460.1642639X-RAY DIFFRACTION100
3.1771-4.00250.15321630.14382677X-RAY DIFFRACTION100
4.0025-46.49960.18481400.14622869X-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)
11.52710.7805-1.93630.7643-0.90262.41670.0372-0.2003-0.0239-0.11120.02280.01180.34610.1798-0.03750.3290.0053-0.07170.2267-0.01620.1857-24.255719.951-8.0774
22.59650.9799-0.75411.81010.26042.4642-0.07450.20120.1156-0.27130.16010.3640.3407-0.1753-0.06330.2547-0.0594-0.09190.17740.06160.1855-36.115224.897-8.9474
31.0388-0.1203-0.25022.09720.35682.22410.00570.0090.0232-0.07290.04940.23040.01540.025-0.05530.1792-0.0284-0.02320.14740.03410.1958-30.457636.4683-6.9838
44.58831.13750.11421.3434-0.23591.34730.0641-0.13690.03170.09550.02770.09460.113-0.0371-0.10040.1988-0.0194-0.01540.14180.00770.1616-28.522431.83665.5305
57.36582.1943-1.22242.5296-0.67782.23620.1659-0.41170.5490.2474-0.03790.3902-0.09610.0733-0.0980.2386-0.00480.00570.1738-0.00830.1835-28.320332.797412.0159
62.1723-0.9728-0.00673.03621.55664.67230.1539-0.0173-0.1437-0.02630.00540.24970.7323-0.0544-0.12220.3307-0.0231-0.05620.20440.03680.1763-32.098315.81976.4749
76.253.67540.44983.7075-0.29391.4420.1676-0.32450.08070.1804-0.1988-0.12070.13620.32570.04370.2768-0.0008-0.00650.30870.01750.1616-17.413328.349214.6496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 124 )
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 191 )
4X-RAY DIFFRACTION4chain 'A' and (resid 193 through 239 )
5X-RAY DIFFRACTION5chain 'A' and (resid 240 through 261 )
6X-RAY DIFFRACTION6chain 'A' and (resid 262 through 295 )
7X-RAY DIFFRACTION7chain 'A' and (resid 296 through 317 )

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