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- PDB-7uhh: Time-Resolved Structure of Metallo Beta-Lactamase L1 in a Complex... -

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Basic information

Entry
Database: PDB / ID: 7uhh
TitleTime-Resolved Structure of Metallo Beta-Lactamase L1 in a Complex with Non-Hydrolyzed Moxalactam (20 ms snapshot)
ComponentsPutative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
KeywordsHYDROLASE / metallo beta lactamase / moxalactam / serial crystallography / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-MX0 / beta-lactamase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia K279a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWilamowski, M. / Kim, Y. / Sherrell, D.A. / Lavens, A. / Henning, R. / Maltseva, N. / Endres, M. / Babnigg, G. / Srajer, V. / 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: Nat Commun / Year: 2022
Title: Time-resolved beta-lactam cleavage by L1 metallo-beta-lactamase.
Authors: Wilamowski, M. / Sherrell, D.A. / Kim, Y. / Lavens, A. / Henning, R.W. / Lazarski, K. / Shigemoto, A. / Endres, M. / Maltseva, N. / Babnigg, G. / Burdette, S.C. / Srajer, V. / Joachimiak, A.
History
DepositionMar 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 25, 2023Group: 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: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7034
Polymers29,2441
Non-polymers4593
Water88349
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)118,81216
Polymers116,9764
Non-polymers1,83612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_445-y-1,-x-1,-z+1/31
Buried area9030 Å2
ΔGint-48 kcal/mol
Surface area38620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.853, 105.853, 99.100
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

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Components

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


Mass: 29243.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia K279a (bacteria)
Strain: K279a / Gene: Smlt2667 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: B2FTM1, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MX0 / (1R,6R,7R)-7-[(2R)-2-carboxypropanamido]-7-methoxy-3-methyl-8-oxo-5-oxa-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid


Mass: 328.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 55.11 %
Crystal growTemperature: 289 K / Method: batch mode
Details: Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate ...Details: Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate pH 8.0, 20% (w/v) PEG3350.

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.02-1.15
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Feb 12, 2020
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.021
21.151
ReflectionResolution: 2.2→33.03 Å / Num. obs: 12926 / % possible obs: 75.7 % / Redundancy: 13.1 % / Biso Wilson estimate: 11.42 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 21.1
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.119 / Num. unique obs: 729
Serial crystallography sample deliveryDescription: Nylon Mesh / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: ALEX mesh holder
Motion control: SmarAct Motors viaPMAC start/stop raster over area
Sample holding: nylon mesh / Support base: xyz stage
Serial crystallography data reductionCrystal hits: 2578 / Frames indexed: 214 / Frames total: 5670 / Lattices indexed: 214

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MOLREPphasing
Precognitiondata reduction
Epinormdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L91

7l91


Resolution: 2.2→33.03 Å / SU ML: 0.4281 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.6803
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.262 599 4.65 %
Rwork0.2234 12288 -
obs0.2252 12887 75.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.63 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 25 50 2061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272060
X-RAY DIFFRACTIONf_angle_d0.58272819
X-RAY DIFFRACTIONf_chiral_restr0.0393315
X-RAY DIFFRACTIONf_plane_restr0.0038372
X-RAY DIFFRACTIONf_dihedral_angle_d19.2095300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.420.37841010.30821793X-RAY DIFFRACTION45.43
2.42-2.770.31751250.28662910X-RAY DIFFRACTION71.82
2.77-3.490.29071710.23823536X-RAY DIFFRACTION87.14
3.49-33.030.18892020.16594049X-RAY DIFFRACTION94.45
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)
10.0934417698352-0.06445770377330.01218846999030.0459013240665-0.01829115884930.02582812282230.007631304645230.03380837015710.0654057078926-0.101698094783-0.0356542108230.00203739928417-0.0417199273234-0.0566693584814-0.01237191732820.0856822904770.0619647173495-0.02551762247560.0316667762871-0.008274016656890.0873795286806-27.0039680571-19.54481221836.98701372016
20.00112693177739-0.000373510022093-0.0006197453864490.0002289572076830.001973595858910.00605668705593-0.00427590421697-0.003329890692460.0012749739079-0.00455413117324-0.00909968058653-0.00868017930496-0.0029567614594-0.00655076266946-0.01864983334450.01581544895690.000369239208190.03048839789470.0605481979628-0.02252101598610.117970089127-40.608575426-27.2282187096.55044877652
30.025606886714-0.0252167611880.02293055783460.0359315012155-0.0119230207090.0315678647909-0.0436879192185-0.02490578728440.0324248567690.0377383176764-0.0395615552394-0.0252124789126-0.0422008096881-0.0199558494819-0.051678188350.1105788867380.06379201971350.006063353177840.082304318644-0.01891008810210.0945068863117-39.3605960625-23.856648310313.1717501758
40.00596432028070.03698334791710.03804954481850.3647515766660.02738570280190.359044355946-0.06926407511920.0745773197550.0816543013877-0.0852794246356-0.1539275547750.0380637338056-0.0534106196490.0233642629431-0.5936432299160.03504369379250.0927118932313-0.0616383395955-0.01311757345620.040986358290.0685549675961-32.2638846821-33.9462994083.54433020555
50.0103764771923-0.0153955861816-0.001500484976550.02141116872560.002568072528470.001094615760170.00154659917950.00328132532716-0.0274254687127-0.00328020720004-0.00599880621607-0.01387350859710.00363516338387-0.005375183110170.005968804040460.05505641528450.0556247312944-0.00364887427690.105466045360.0501234759110.14726795648-15.4446874875-36.4471610328-5.45273066793
60.00932623920726-0.000296425001786-0.001024372908930.002885795429110.005200736626410.00911180391981-0.00832587039072-0.00817961640449-0.0102909206881-0.0192612707664-0.000855527624801-0.009445975101450.001769107545910.0176347211565-0.01757340857110.1999001752680.06824355833780.07713909195770.1663947987260.04108838452310.0969880984365-23.7744753116-36.7132562504-12.6322661754
70.0142299400908-0.0151056609219-0.009083086554250.0301589597885-0.02159176317890.073607442790.0225446448461-0.008033478278270.003064306875590.01225932911850.0358339286460.0254168851868-0.0538319852708-0.02747765207430.140573148760.09417400041310.0973342148558-0.04078090938210.07730596041010.006097524896060.1584751903-33.8835454731-19.1948186971-7.41885068927
80.0101345724890.03435598669960.0263162804650.1267117597240.09403380663930.0701704632827-0.0629198506083-0.00196308480042-0.0239717369908-0.0107560216866-0.0753783453918-0.0204989404169-0.01195390117120.0831460468737-0.07480895943570.2114240496080.01028827888140.01919519840330.152788349940.07440887738670.13746407761-17.8773410699-28.5277232177-14.6361393979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 102 )
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 204 )
5X-RAY DIFFRACTION5chain 'A' and (resid 205 through 222 )
6X-RAY DIFFRACTION6chain 'A' and (resid 223 through 235 )
7X-RAY DIFFRACTION7chain 'A' and (resid 236 through 266 )
8X-RAY DIFFRACTION8chain 'A' and (resid 267 through 287 )

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