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- PDB-9jna: Crystal Structure of SME-1 E166A mutant in complex with Meropenem -

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Basic information

Entry
Database: PDB / ID: 9jna
TitleCrystal Structure of SME-1 E166A mutant in complex with Meropenem
Componentsbeta-lactamase
KeywordsHYDROLASE / Carbapenemase / muatant / complex
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
Chem-DWZ / DI(HYDROXYETHYL)ETHER / 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
Board of Research in Nuclear Sciences (BRNS)54/14/03/2023-BRNS India
Indian Council of Medical ResearchEM/Dev/IG/20/0773/2023 India
CitationJournal: To Be Published
Title: Crystal Structure of SME-1 E166A mutant in complex with Meropenem
Authors: Dhankhar, K. / Hazra, S.
History
DepositionSep 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 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
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0279
Polymers60,6912
Non-polymers1,3367
Water1,45981
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0314
Polymers30,3451
Non-polymers6863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11160 Å2
MethodPISA
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9965
Polymers30,3451
Non-polymers6514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-12 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.311, 51.08, 130.829
Angle α, β, γ (deg.)90, 92.177, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein beta-lactamase / SME E166A


Mass: 30345.266 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 88 molecules

#2: Chemical ChemComp-DWZ / (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.06 Å3/Da / Density % sol: 38.43 %
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: Jul 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→25.54 Å / Num. obs: 18976 / % possible obs: 99.9 % / Redundancy: 8.7 % / CC1/2: 0.996 / Net I/σ(I): 15.2
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 1940 / CC1/2: 0.941

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→25.54 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.845 / SU B: 21.264 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / ESU R Free: 0.314 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2631 973 5.131 %
Rwork0.1874 17990 -
all0.191 --
obs-18963 99.847 %
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: 16.634 Å2
Baniso -1Baniso -2Baniso -3
1--1.022 Å2-0 Å20.2 Å2
2--0.408 Å20 Å2
3---0.598 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 87 81 4276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124274
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.825757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5735534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.777536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99910739
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.28910185
X-RAY DIFFRACTIONr_chiral_restr0.1360.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023202
X-RAY DIFFRACTIONr_nbd_refined0.2280.22045
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22948
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2182
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.29
X-RAY DIFFRACTIONr_mcbond_it0.8850.5882145
X-RAY DIFFRACTIONr_mcangle_it1.4971.0532676
X-RAY DIFFRACTIONr_scbond_it1.1090.6452129
X-RAY DIFFRACTIONr_scangle_it1.8441.1693081
X-RAY DIFFRACTIONr_lrange_it6.1276.8226592
X-RAY DIFFRACTIONr_rigid_bond_restr2.24134274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.333820.2221273X-RAY DIFFRACTION99.9263
2.462-2.5290.33760.2141259X-RAY DIFFRACTION100
2.529-2.6010.306680.1981277X-RAY DIFFRACTION100
2.601-2.680.217790.1841170X-RAY DIFFRACTION100
2.68-2.7670.281750.1981166X-RAY DIFFRACTION100
2.767-2.8630.331570.1971156X-RAY DIFFRACTION100
2.863-2.970.252500.21091X-RAY DIFFRACTION100
2.97-3.0890.281480.2021048X-RAY DIFFRACTION100
3.089-3.2250.307390.21029X-RAY DIFFRACTION100
3.225-3.3790.245450.189993X-RAY DIFFRACTION100
3.379-3.5590.242520.186930X-RAY DIFFRACTION99.8983
3.559-3.770.263420.187871X-RAY DIFFRACTION100
3.77-4.0240.247430.169861X-RAY DIFFRACTION100
4.024-4.3380.236490.156745X-RAY DIFFRACTION100
4.338-4.7380.197440.162715X-RAY DIFFRACTION99.8684
4.738-5.2750.272320.161670X-RAY DIFFRACTION100
5.275-6.0480.288250.199583X-RAY DIFFRACTION100
6.048-7.3050.274390.198498X-RAY DIFFRACTION100
7.305-9.9330.17210.156392X-RAY DIFFRACTION99.7585
9.933-25.540.26770.195263X-RAY DIFFRACTION98.5401
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)
11.06260.4444-0.49441.5613-0.35891.6261-0.0389-0.0310.0186-0.14410.0477-0.02240.01630.004-0.00880.07190.0027-0.02140.0143-0.00260.011613.97450.099950.0797
21.4967-0.5652-0.31111.98830.2171.56220.03850.10060.04990.046-0.0453-0.02010.00550.03280.00680.079-0.053-0.00870.0580.00980.003517.445823.412915.4496
Refinement TLS groupSelection: ALL

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