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- PDB-7o0o: Crystal structure of the B3 metallo-beta-lactamase L1 with hydrol... -

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Basic information

Entry
Database: PDB / ID: 7o0o
TitleCrystal structure of the B3 metallo-beta-lactamase L1 with hydrolysed ertapenem
ComponentsMetallo-beta-lactamase L1
KeywordsANTIMICROBIAL PROTEIN / antibiotic / ligand / metalloprotein / lactamase / carbapenem
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / 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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-9XS / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI100560 United States
CitationJournal: J.Chem.Inf.Model. / Year: 2021
Title: Crystallography and QM/MM Simulations Identify Preferential Binding of Hydrolyzed Carbapenem and Penem Antibiotics to the L1 Metallo-beta-Lactamase in the Imine Form.
Authors: Twidale, R.M. / Hinchliffe, P. / Spencer, J. / Mulholland, A.J.
History
DepositionMar 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 2.0Dec 1, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Feb 16, 2022Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation
Revision 2.2Jan 31, 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

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Assembly

Deposited unit
A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7777
Polymers28,8951
Non-polymers8826
Water5,170287
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)119,10628
Polymers115,5784
Non-polymers3,52824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Unit cell
Length a, b, c (Å)105.803, 105.803, 98.149
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-303-

ZN

21A-411-

HOH

31A-440-

HOH

41A-656-

HOH

51A-662-

HOH

61A-673-

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 (E. coli) / References: UniProt: P52700, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-9XS / (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid


Mass: 493.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N3O8S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 277 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.45→46.57 Å / Num. obs: 57760 / % possible obs: 100 % / Redundancy: 36.7 % / CC1/2: 0.999 / Rpim(I) all: 0.024 / Net I/σ(I): 18.2
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 30.3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2805 / CC1/2: 0.804 / Rpim(I) all: 0.54 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EVD

5evd


Resolution: 1.45→32.72 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1692 2805 4.87 %
Rwork0.1543 54821 -
obs0.155 57626 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.29 Å2 / Biso mean: 28.3419 Å2 / Biso min: 11.53 Å2
Refinement stepCycle: final / Resolution: 1.45→32.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 71 287 2359
Biso mean--66.9 35.73 -
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.470.29661320.28642664279698
1.47-1.50.26481390.258126682807100
1.5-1.530.27371500.225626732823100
1.53-1.560.24681440.224926992843100
1.56-1.60.23411220.211526982820100
1.6-1.630.18191470.189127002847100
1.63-1.670.22621570.188826842841100
1.67-1.720.22091470.186127122859100
1.72-1.770.17811230.171627152838100
1.77-1.830.20021480.169327182866100
1.83-1.890.19491380.157527242862100
1.89-1.970.18171450.154427192864100
1.97-2.060.17771470.148627222869100
2.06-2.170.15491410.142627572898100
2.17-2.30.1441210.137827622883100
2.3-2.480.14851200.132127892909100
2.48-2.730.1361620.135927532915100
2.73-3.120.17071360.142428032939100
3.12-3.930.14491560.134328312987100
3.93-32.720.15641300.154430303160100
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)
12.8650.4617-1.73081.0163-0.47551.4909-0.0094-0.0854-0.05860.03170.09230.20160.1398-0.0172-0.04640.1882-0.0258-0.01240.15680.02780.1896-30.44421.229-8.296
26.88172.86131.10334.21531.4462.8813-0.10440.19380.1997-0.06080.11520.44740.1089-0.21860.0120.1465-0.03590.00430.13510.07530.1622-35.69428.785-9.277
30.7506-0.37050.03011.72730.12971.2595-0.0522-0.0194-0.06050.04610.1120.1798-0.01770.0083-0.03260.1404-0.01280.01430.14920.03170.1543-30.44736.754-6.89
48.66842.9101-0.26322.7891-0.26340.7994-0.0721-0.2038-0.14030.35060.13230.13310.1021-0.0339-0.03950.22980.03790.04080.17050.04450.1301-28.632.0415.537
54.35245.7914-4.37568.2924-5.11275.83390.1217-0.15170.32260.53470.03840.2742-0.22360.0441-0.07930.29230.06850.00990.20850.01250.1324-24.68636.02613.521
62.6317-0.3226-2.19762.2681.71715.7494-0.043-0.125-0.1180.1740.06010.24680.3776-0.0107-0.03620.26640.01680.04760.20880.09820.2166-33.23618.7537.334
74.52196.2842-0.43947.8249-0.77040.27350.0379-0.3782-0.18870.4950.0246-0.29040.05180.0471-0.02260.29090.0642-0.01030.2940.07410.167-17.41528.47914.558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:69 )A2 - 69
2X-RAY DIFFRACTION2( CHAIN A AND RESID 70:92 )A70 - 92
3X-RAY DIFFRACTION3( CHAIN A AND RESID 93:156 )A93 - 156
4X-RAY DIFFRACTION4( CHAIN A AND RESID 157:201 )A157 - 201
5X-RAY DIFFRACTION5( CHAIN A AND RESID 202:215 )A202 - 215
6X-RAY DIFFRACTION6( CHAIN A AND RESID 216:245 )A216 - 245
7X-RAY DIFFRACTION7( CHAIN A AND RESID 246:267 )A246 - 267

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