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- PDB-6u0z: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrop... -

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Basic information

Entry
Database: PDB / ID: 6u0z
TitleCrystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with the hydrolyzed penicillin G
ComponentsPutative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
KeywordsHYDROLASE / lactam antibiotics / penicillin G / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / 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
sucrose / DI(HYDROXYETHYL)ETHER / Chem-PNK / beta-lactamase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with the hydrolyzed penicillin G.
Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6089
Polymers29,1731
Non-polymers1,4358
Water3,999222
1
A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,43336
Polymers116,6914
Non-polymers5,74232
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area13610 Å2
ΔGint-71 kcal/mol
Surface area39800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.759, 104.759, 98.434
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-305-

ZN

21A-452-

HOH

31A-607-

HOH

41A-610-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)


Mass: 29172.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: Smlt2667 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: B2FTM1, beta-lactamase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 228 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-PNK / (2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / Penicillin, hydroxylated form


Mass: 352.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 38907 / % possible obs: 100 % / Redundancy: 20.8 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 44.7
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 16 % / Rmerge(I) obs: 0.943 / Mean I/σ(I) obs: 4 / Num. unique obs: 1892 / CC1/2: 0.894 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 6U0Y

6u0y


Resolution: 1.65→34.3 Å / SU ML: 0.1575 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3477
RfactorNum. reflection% reflectionSelection details
Rfree0.1806 1891 4.9 %random
Rwork0.1576 ---
obs0.1587 38598 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.53 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 59 222 2294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582255
X-RAY DIFFRACTIONf_angle_d1.00423094
X-RAY DIFFRACTIONf_chiral_restr0.0557347
X-RAY DIFFRACTIONf_plane_restr0.0057402
X-RAY DIFFRACTIONf_dihedral_angle_d15.08731343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.2361330.19262595X-RAY DIFFRACTION99.53
1.69-1.740.24271400.18532538X-RAY DIFFRACTION99.67
1.74-1.790.20141350.18022586X-RAY DIFFRACTION99.6
1.79-1.850.22271490.16712565X-RAY DIFFRACTION99.27
1.85-1.910.19291340.16972598X-RAY DIFFRACTION99.45
1.91-1.990.19851150.16952590X-RAY DIFFRACTION99.3
1.99-2.080.19481380.16142584X-RAY DIFFRACTION99.38
2.08-2.190.23061340.15812614X-RAY DIFFRACTION99.42
2.19-2.320.18861320.15432610X-RAY DIFFRACTION99.2
2.32-2.50.18131430.16282589X-RAY DIFFRACTION98.81
2.5-2.760.18331280.16812644X-RAY DIFFRACTION99
2.76-3.150.18341320.15992634X-RAY DIFFRACTION98.93
3.15-3.970.13461410.13652690X-RAY DIFFRACTION98.95
3.97-34.30.16711370.15162870X-RAY DIFFRACTION99.47
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)
10.1577895782320.40014069615-0.4407989873364.59156055361-3.008162981972.208291306510.01806987131390.0115390346643-0.05034713611090.0820815315841-0.197549370555-0.261964719273-0.00621723309690.1618422909730.1544262120610.1818394422750.01870465740830.005732725573670.1703924222390.00362896024040.189366914163-29.4931232565-11.76181841868.59657265131
23.265126118940.239195876788-0.8256473564924.05223791693-0.5392579950413.44539535568-0.02877735038340.121767123027-0.191271212527-0.160751066372-0.0501121993627-0.002065427980650.1940161223140.09856082484980.06209377827110.1416645028790.03239682290620.0003274171622090.09045775861420.004747520468990.118183672071-37.4131595197-20.39901321067.65841228178
31.08738277121-0.172421166921-0.1795158971420.9193418642180.09115552731951.15260678873-0.02677507718310.0617350896051-0.12434912705-0.0284352496207-0.03905849552910.05286966291250.137922138886-0.003267242881890.04060876969140.1374669149170.01051745394220.001423785362620.08574224115830.002282044446810.123315722104-45.1205709162-13.453178437512.2537057647
44.88094635032-1.85456056474-0.6161169133797.737155262880.319611999631.67437591197-0.0676142299576-0.06905780856910.4721624100290.1406515402130.0806787315907-0.249251952835-0.1896611284880.04817151214940.001365812470630.173882811176-0.00302592344002-0.04709669538810.1152027409720.005117309152550.11560367146-39.38522027425.2406797601722.0413957437
51.427896643440.0548004835767-0.6774808237996.43068272667-0.0672055412172.51326497177-0.0653700066762-0.142154397906-0.06608995509970.4951199076920.04575657099380.2640565979420.0220001469495-0.07285591171380.0293866298590.1334398887760.0198378913208-0.0236348448620.1264967110510.008691423165120.0936587223231-42.6040822875-7.9718683882828.4984565005
63.849580853460.0826834689194-0.7349055094973.05896004825-0.4238125703243.67974022571-0.00392593886985-0.000128725233592-0.2268099282360.09972576390180.0834080509153-0.2528353136920.4446119193320.5788165957550.05994466621040.1810827562490.0621623531418-0.02700669837990.1698548455310.01670190354560.154531831148-29.6066890971-19.82676330922.8660334292
74.663522925923.915180811270.7049723613937.006451829271.265691928792.42175329642-0.0389891343508-0.1748301979020.2087370364110.4790067794360.035263207659-0.136038277959-0.1099773707440.1478926355150.008589441159240.2167919676780.0380192542929-0.06807259654940.1987321749290.0029630810810.181121437768-33.2418694831-1.4836459099130.926178254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 90 )
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 204 )
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 222 )
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 244 )
6X-RAY DIFFRACTION6chain 'A' and (resid 245 through 266 )
7X-RAY DIFFRACTION7chain 'A' and (resid 267 through 288 )

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