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- PDB-7uhr: Time-Resolved Structure of Metallo Beta-Lactamase L1 Before React... -

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Basic information

Entry
Database: PDB / ID: 7uhr
TitleTime-Resolved Structure of Metallo Beta-Lactamase L1 Before Reaction (Dark-Set)
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
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

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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)29,3092
Polymers29,2441
Non-polymers651
Water1,26170
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)117,2378
Polymers116,9764
Non-polymers2624
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 area9580 Å2
ΔGint-189 kcal/mol
Surface area39040 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 / Plasmid: pMCSG53 / 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.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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 11, 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→26.01 Å / Num. obs: 12094 / % possible obs: 70.8 % / Redundancy: 9.2 % / Biso Wilson estimate: 13.61 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 20.2
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.104 / Num. unique obs: 593
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: 1210 / Frames indexed: 143 / Frames total: 5000 / Lattices indexed: 143

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Precognitiondata reduction
Epinormdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L52

7l52


Resolution: 2.2→26.01 Å / SU ML: 0.2711 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.3021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2436 558 4.64 %
Rwork0.2218 11473 -
obs0.2228 12031 70.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.93 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 1 72 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00132036
X-RAY DIFFRACTIONf_angle_d0.4012782
X-RAY DIFFRACTIONf_chiral_restr0.0375312
X-RAY DIFFRACTIONf_plane_restr0.0036366
X-RAY DIFFRACTIONf_dihedral_angle_d17.9704725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.420.2723800.27631540X-RAY DIFFRACTION38.73
2.42-2.770.2941110.28312608X-RAY DIFFRACTION64.55
2.77-3.490.29561680.24423361X-RAY DIFFRACTION82.7
3.49-26.010.19491990.17463964X-RAY DIFFRACTION92.55
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)
13.2663340925-1.364579618341.455561916550.70432664749-0.7229422036831.19790956092-0.2027766459970.2505581697110.330655917872-0.07626220821360.10938896184-0.249537053598-0.5027659211660.1513629460460.0461642586360.1311294501560.0470581590323-0.0156538740810.270593869737-0.04171479594140.216008643193-26.9570475787-19.59166732687.03135793924
21.00775011697-0.630639907460.4149906082741.76006981476-0.007004231255681.857206111920.0543625979082-0.1862383926440.06388249424880.0295209110609-0.03584299958810.0164107141612-0.222228451175-0.0785259281034-0.004180591756420.150851949256-0.000520008282322-0.00701095426630.1928123833480.004883685600380.115032045534-35.2322069775-29.088071261410.4827644348
30.330855210681-0.2745842747310.2191220425381.382512511790.3190349633051.43219118348-0.03686043257250.00608298749791-0.0818496507228-0.0934368902719-0.1041386920130.02673906443980.02350202265220.01575786979910.1819632041720.140856541120.02706252677060.02501373823830.1535180294230.02587585467850.14848467232-29.3194282159-37.03042806893.08714850782
42.76023905107-0.4529233278890.1290128105931.295038316440.407036979850.651965026282-0.1673963607560.3609911411910.175626864996-0.160777387065-0.0152816110693-0.142053908803-0.237976060910.02168402470560.1072208024190.2510530926460.051032987081-0.01763464586010.1721731915240.08550076193390.166698117352-29.8312237959-31.5343064786-5.7293111577
51.798626982-0.573527901734-0.1107276090011.14663883353-0.1606893911542.135596841310.1197180365850.09928306865730.183275767039-0.4835256618450.012370570873-0.111382605332-0.2690132661920.0918455590531-0.07302568733090.2646892138460.0853712552262-0.002909684345880.1870853755780.04098617998610.117213458611-30.4948080326-25.0823160212-9.15280702042
66.01149058724-1.48381170777-1.145716151233.39351921972-0.008004619400163.39503820671-0.18093989972-0.0407647005313-0.61101476577-0.182645193067-0.209992011199-0.176967732945-0.2561382822580.6346720659460.2876957652330.2980269850190.04125471067290.0107848361390.3280556302860.07168878482180.220860145539-17.9108256034-28.549410736-14.6538821471
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 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 185 )
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 222 )
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 266 )
6X-RAY DIFFRACTION6chain 'A' and (resid 267 through 287 )

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