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- PDB-7bj9: Structure of Sfh-I with 2-Mercaptomethyl-thiazolidine L-anti-1a -

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Basic information

Entry
Database: PDB / ID: 7bj9
TitleStructure of Sfh-I with 2-Mercaptomethyl-thiazolidine L-anti-1a
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance / lactamase / zinc / inhibitor
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 2. / 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-TWW / Beta-lactamase
Similarity search - Component
Biological speciesSerratia fonticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21000590023 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: Acs Infect Dis. / Year: 2021
Title: 2-Mercaptomethyl Thiazolidines (MMTZs) Inhibit All Metallo-beta-Lactamase Classes by Maintaining a Conserved Binding Mode.
Authors: Hinchliffe, P. / Moreno, D.M. / Rossi, M.A. / Mojica, M.F. / Martinez, V. / Villamil, V. / Spellberg, B. / Drusano, G.L. / Banchio, C. / Mahler, G. / Bonomo, R.A. / Vila, A.J. / Spencer, J.
History
DepositionJan 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Beta-lactamase
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4538
Polymers52,6362
Non-polymers8186
Water7,819434
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7274
Polymers26,3181
Non-polymers4093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7274
Polymers26,3181
Non-polymers4093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.083, 88.071, 72.061
Angle α, β, γ (deg.)90.000, 90.513, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-lactamase / Metallo-beta-lactamase class B2 Sfh-I


Mass: 26317.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia fonticola (bacteria) / Gene: sfhI / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RMI1, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TWW / (2~{S},4~{R})-2-ethoxycarbonyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid


Mass: 251.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium acetate, 27% w/v PEG 3350, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.21→72.06 Å / Num. obs: 125135 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 10.6175657012 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.05 / Net I/σ(I): 8.9
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 39153 / CC1/2: 0.566 / Rpim(I) all: 0.901 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ew0

5ew0


Resolution: 1.21000590023→72.0582070932 Å / SU ML: 0.0984097092555 / Cross valid method: FREE R-VALUE / σ(F): 1.34746974891 / Phase error: 15.6291406383
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.152439983724 6200 4.96087311367 %
Rwork0.13597287523 118778 -
obs0.136814275367 124978 99.67778469 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.9873267087 Å2
Refinement stepCycle: LAST / Resolution: 1.21000590023→72.0582070932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 44 434 4136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01022481928373992
X-RAY DIFFRACTIONf_angle_d1.204358099815458
X-RAY DIFFRACTIONf_chiral_restr0.26882263422602
X-RAY DIFFRACTIONf_plane_restr0.00787246177923713
X-RAY DIFFRACTIONf_dihedral_angle_d16.83807798691500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21000590023-1.22380.2250549939961850.2001114630183956X-RAY DIFFRACTION98.5483103284
1.2238-1.23820.2314542656881990.1969478667533906X-RAY DIFFRACTION99.0588803089
1.2382-1.25330.2421396040062030.1959792003663877X-RAY DIFFRACTION98.8611582263
1.2533-1.26910.2254929104691980.1935237860013947X-RAY DIFFRACTION98.902409926
1.2691-1.28580.2244738667621980.1899373062963900X-RAY DIFFRACTION99.0094225658
1.2858-1.30340.2029273753841910.1705047416083942X-RAY DIFFRACTION99.2078732597
1.3034-1.32210.2002489087522120.1674304886023983X-RAY DIFFRACTION99.5727510088
1.3221-1.34180.1953066499982020.1550905060063926X-RAY DIFFRACTION99.4459166466
1.3418-1.36280.1770564792312040.1579818147713932X-RAY DIFFRACTION99.5427196149
1.3628-1.38510.1882136835871630.1554793697054011X-RAY DIFFRACTION99.5468638207
1.3851-1.4090.1784886425541700.1471806492663962X-RAY DIFFRACTION99.7104247104
1.409-1.43460.1587927052381800.1432196025723995X-RAY DIFFRACTION99.6895893028
1.4346-1.46220.1791138750472070.1388621451863940X-RAY DIFFRACTION99.7354497354
1.4622-1.49210.1448882788511600.1274330632414026X-RAY DIFFRACTION99.9283838625
1.4921-1.52450.1436199602782070.1244732042773933X-RAY DIFFRACTION99.8793727382
1.5245-1.560.1502595941792150.1169150493433994X-RAY DIFFRACTION99.9525053431
1.56-1.5990.1538084409312190.1181808801673932X-RAY DIFFRACTION99.9277804526
1.599-1.64220.1508622488942270.1180538115423970X-RAY DIFFRACTION100
1.6422-1.69060.1570647359232270.1219002335973920X-RAY DIFFRACTION99.9758919961
1.6906-1.74510.172062368442480.1218569905253951X-RAY DIFFRACTION100
1.7451-1.80750.1556944106622000.1215594270033969X-RAY DIFFRACTION100
1.8075-1.87990.1427225749312510.123776565593904X-RAY DIFFRACTION100
1.8799-1.96540.1573179945482040.1206960560764007X-RAY DIFFRACTION100
1.9654-2.06910.1363069082732400.1227200339753950X-RAY DIFFRACTION100
2.0691-2.19870.1423364971881750.1216417260544017X-RAY DIFFRACTION100
2.1987-2.36850.1426490490232600.1252598322643922X-RAY DIFFRACTION100
2.3685-2.60680.1520678284572170.1318861908983964X-RAY DIFFRACTION100
2.6068-2.98410.1578190905142160.1449755850523986X-RAY DIFFRACTION100
2.9841-3.75960.1404641772262180.1338220963364002X-RAY DIFFRACTION100
3.7596-72.05820709320.1185384165022040.1385637068384054X-RAY DIFFRACTION99.8592870544

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