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- PDB-9ivl: Crystal Structure of SME-1 E166A mutant in complex with Biapenem -

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Basic information

Entry
Database: PDB / ID: 9ivl
TitleCrystal Structure of SME-1 E166A mutant in complex with Biapenem
Componentsbeta-lactamase
KeywordsHYDROLASE / Complex / Carbapenem
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / nucleosome binding / NADP binding / oxidoreductase activity / chromatin / DNA binding
Similarity search - Function
: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-BMG / Oxidoreductase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDhankhar, K. / Hazra, S.
Funding support India, 2items
OrganizationGrant numberCountry
Indian Council of Medical ResearchEM/Dev/IG/20/0773/2023 India
Board of Research in Nuclear Sciences (BRNS)54/14/03/2023-BRNS India
CitationJournal: To Be Published
Title: Crystal Structure of SME-1 E166A mutant in complex with Biapenem
Authors: Dhankhar, K. / Hazra, S.
History
DepositionJul 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8254
Polymers30,3451
Non-polymers4803
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-11 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.605, 51.728, 88.226
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein beta-lactamase / SME E166A


Mass: 30345.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: sme-2, blaSME-1, blaSME-4, blaSME1, SME12620_22 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54488, beta-lactamase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-BMG / (4R,5S)-3-(6,7-dihydro-5H-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-ylsulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-meth yl-4,5-dihydro-1H-pyrrole-2-carboxylate / (4R,5S)-3-(6,7-dihydro-5H-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-ylthio)-5-((2S,3R)-3-hydroxy-1-oxobutan-2-yl)-4- methyl-4,5-dihydro-1H-pyrrole-2-carboxylate


Mass: 352.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20N4O4S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
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: 1.73 Å3/Da / Density % sol: 29.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M lithium chloride, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Oct 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.4→22.37 Å / Num. obs: 40678 / % possible obs: 99.3 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 18.6
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 1905 / CC1/2: 0.887

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→22.37 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.24 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.062
RfactorNum. reflection% reflection
Rfree0.1771 1989 4.897 %
Rwork0.1388 38629 -
all0.141 --
obs-40618 99.158 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 9.594 Å2
Baniso -1Baniso -2Baniso -3
1--2.456 Å2-0 Å2-0 Å2
2--1.101 Å2-0 Å2
3---1.355 Å2
Refinement stepCycle: LAST / Resolution: 1.4→22.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 31 236 2311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122152
X-RAY DIFFRACTIONr_angle_refined_deg2.0971.8312908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0115268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.6258.15819
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6910373
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.9171093
X-RAY DIFFRACTIONr_chiral_restr0.1260.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021617
X-RAY DIFFRACTIONr_nbd_refined0.2150.21074
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2170
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.220.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4470.231
X-RAY DIFFRACTIONr_mcbond_it2.2410.6731063
X-RAY DIFFRACTIONr_mcangle_it3.3621.2091328
X-RAY DIFFRACTIONr_scbond_it4.0190.8851089
X-RAY DIFFRACTIONr_scangle_it5.7011.5391578
X-RAY DIFFRACTIONr_lrange_it21.98211.5623519
X-RAY DIFFRACTIONr_rigid_bond_restr5.74532152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.1951460.1582703X-RAY DIFFRACTION95.9259
1.436-1.4750.1691490.1322696X-RAY DIFFRACTION97.9346
1.475-1.5180.1891250.1322622X-RAY DIFFRACTION97.8974
1.518-1.5650.1861220.1322575X-RAY DIFFRACTION98.4307
1.565-1.6160.1621260.1222519X-RAY DIFFRACTION98.9895
1.616-1.6720.1721480.1212419X-RAY DIFFRACTION99.5347
1.672-1.7350.1651260.1262359X-RAY DIFFRACTION99.7191
1.735-1.8050.1811310.1292265X-RAY DIFFRACTION99.9166
1.805-1.8850.1961280.132178X-RAY DIFFRACTION99.9567
1.885-1.9760.173940.1332121X-RAY DIFFRACTION100
1.976-2.0820.1821140.1351994X-RAY DIFFRACTION100
2.082-2.2070.1891030.141907X-RAY DIFFRACTION100
2.207-2.3580.196700.1331830X-RAY DIFFRACTION100
2.358-2.5450.164630.1431685X-RAY DIFFRACTION100
2.545-2.7840.169920.1531554X-RAY DIFFRACTION100
2.784-3.1060.205670.1631420X-RAY DIFFRACTION99.9328
3.106-3.5760.18680.1441257X-RAY DIFFRACTION100
3.576-4.3510.162570.1321094X-RAY DIFFRACTION100
4.351-6.0410.137350.146873X-RAY DIFFRACTION100
6.041-22.370.174250.174558X-RAY DIFFRACTION100

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