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- PDB-9iow: Crystal Structure of SME-1 E166A Mutant in complex with Cefaclor -

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Basic information

Entry
Database: PDB / ID: 9iow
TitleCrystal Structure of SME-1 E166A Mutant in complex with Cefaclor
Componentsbeta-lactamase
KeywordsHYDROLASE / Complex / Carbapenemase mutant / Cephalosporin
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
: / Beta-lactamase SME-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDhankhar, K. / Hazra, S.
Funding support India, 2items
OrganizationGrant numberCountry
Indian Council of Medical ResearchEM/Dev/IG/20/773/2023 India
Board of Research in Nuclear Sciences (BRNS)54/10/3/2023-BRNS India
CitationJournal: To Be Published
Title: Crystal Structure of SME-1 E166A Mutant in complex with Cefaclor
Authors: Dhankhar, K. / Hazra, S.
History
DepositionJul 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 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)30,8024
Polymers30,3451
Non-polymers4573
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area10910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.297, 50.788, 61.91
Angle α, β, γ (deg.)90, 98.634, 90
Int Tables number4
Space group name H-MP1211

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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-Q6R / (R)-2-((R)-((R)-2-amino-2-phenylacetamido)(carboxy)methyl)-5-chloro-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / cefaclor


Mass: 385.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16ClN3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.86 Å3/Da / Density % sol: 34.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, 0.2M Lithium Chloride

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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: Jun 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→23.46 Å / Num. obs: 8331 / % possible obs: 97 % / Redundancy: 3.9 % / CC1/2: 0.993 / Net I/σ(I): 10.9
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 855 / CC1/2: 0.925

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→21.476 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.881 / SU B: 21.918 / SU ML: 0.226 / Cross valid method: FREE R-VALUE / ESU R Free: 0.335
RfactorNum. reflection% reflection
Rfree0.2624 389 4.675 %
Rwork0.1509 7932 -
all0.156 --
obs-8321 96.666 %
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: 22.131 Å2
Baniso -1Baniso -2Baniso -3
1--0.526 Å20 Å20.49 Å2
2---1.32 Å2-0 Å2
3---1.623 Å2
Refinement stepCycle: LAST / Resolution: 2.4→21.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 26 43 2127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0122120
X-RAY DIFFRACTIONr_angle_refined_deg2.7611.8242858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3065266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.5926.66718
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.67310373
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.5991092
X-RAY DIFFRACTIONr_chiral_restr0.1890.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021606
X-RAY DIFFRACTIONr_nbd_refined0.2420.21068
X-RAY DIFFRACTIONr_nbtor_refined0.310.21461
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2103
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3540.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.27
X-RAY DIFFRACTIONr_mcbond_it3.1671.0991067
X-RAY DIFFRACTIONr_mcangle_it5.1141.9771332
X-RAY DIFFRACTIONr_scbond_it3.8031.1631053
X-RAY DIFFRACTIONr_scangle_it5.7822.1111526
X-RAY DIFFRACTIONr_lrange_it10.82413.4453364
X-RAY DIFFRACTIONr_rigid_bond_restr5.20532120
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.292350.1725570.1796230.9480.98295.02410.158
2.462-2.5280.35270.165680.1686180.9110.98396.27830.143
2.528-2.6010.46230.1675280.1785710.9130.98296.49740.146
2.601-2.6790.321340.1515370.1615870.9420.98797.27430.135
2.679-2.7660.242280.1495080.1545510.960.98797.27770.132
2.766-2.8610.208200.1595030.1615350.980.98497.7570.142
2.861-2.9670.284220.1635120.1685460.950.98297.80220.144
2.967-3.0860.287270.1464460.1534850.9370.98697.52580.13
3.086-3.220.279140.1464640.154890.950.98697.75050.132
3.22-3.3730.236170.154260.1544540.9760.98597.57710.134
3.373-3.5510.256180.1464140.1514420.960.98797.73760.135
3.551-3.760.242150.1513940.1544170.9670.98798.08150.144
3.76-4.0110.225190.1453710.1494010.9760.98797.25690.138
4.011-4.320.259200.1433480.1493760.9490.98897.87230.136
4.32-4.7130.189140.143180.1423380.9850.98898.22490.134
4.713-5.2380.193170.1332840.1373070.9810.98998.04560.127
5.238-5.9890.332110.162640.1652840.9340.98596.8310.151
5.989-7.1960.273100.152200.1542450.9610.98693.87760.143
7.196-9.650.264110.1451620.1511930.9820.98889.63730.147
9.65-21.4760.21970.1751070.1781320.9750.98386.36360.178
Refinement TLS params.Method: refined / Origin x: 14.5071 Å / Origin y: -0.0038 Å / Origin z: 15.1842 Å
111213212223313233
T0.021 Å20.0089 Å2-0.0059 Å2-0.0761 Å20.0003 Å2--0.0065 Å2
L1.6236 °20.581 °20.2592 °2-2.0448 °20.3103 °2--1.4238 °2
S-0.024 Å °0.0548 Å °-0.0047 Å °-0.1182 Å °0.0506 Å °-0.0211 Å °-0.0511 Å °0.0525 Å °-0.0266 Å °
Refinement TLS groupSelection: ALL

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