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

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Basic information

Entry
Database: PDB / ID: 7uhp
TitleTime-Resolved Structure of Metallo Beta-Lactamase L1 in a Complex with Cleaved Moxalactam (2000 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-XQP / beta-lactamase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia K279a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_scat_Cromer_Mann_a5 / _atom_type.pdbx_scat_Cromer_Mann_b5 ..._atom_type.pdbx_scat_Cromer_Mann_a5 / _atom_type.pdbx_scat_Cromer_Mann_b5 / _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)29,9134
Polymers29,2441
Non-polymers6693
Water81145
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)119,65316
Polymers116,9764
Non-polymers2,67712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area9020 Å2
ΔGint-46 kcal/mol
Surface area38280 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.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XQP / (2R)-2-[(R)-carboxy{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}methoxymethyl]-5-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-3,6-dihydro-2H-1,3-oxazine-4-carboxylic acid


Mass: 538.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N6O10S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: Mar 3, 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→33.65 Å / Num. obs: 11732 / % possible obs: 68.6 % / Redundancy: 12.8 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.161 / Net I/σ(I): 18.1
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.093 / Num. unique obs: 448
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: 4025 / Frames indexed: 265 / Frames total: 7713 / Lattices indexed: 265

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Processing

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

7l91


Resolution: 2.6→33.65 Å / SU ML: 0.5345 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.7612
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2754 424 4.71 %
Rwork0.2506 8571 -
obs0.2518 8995 85.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 4.81 Å2
Refinement stepCycle: LAST / Resolution: 2.6→33.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 26 47 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222060
X-RAY DIFFRACTIONf_angle_d0.50542817
X-RAY DIFFRACTIONf_chiral_restr0.0402315
X-RAY DIFFRACTIONf_plane_restr0.0036372
X-RAY DIFFRACTIONf_dihedral_angle_d20.6485739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.980.40441200.32932359X-RAY DIFFRACTION72.53
2.98-3.750.29611320.26342926X-RAY DIFFRACTION88.13
3.75-33.650.19491720.19833286X-RAY DIFFRACTION94.25

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