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- PDB-9il8: Crystal Structure of SME-1 Class A Carbapenemase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9il8
TitleCrystal Structure of SME-1 Class A Carbapenemase in complex with Durlobactam
Componentsbeta-lactamase
KeywordsHYDROLASE / Acyl Enzyme Complex / Carbapenemase / DBO
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-JXG / DI(HYDROXYETHYL)ETHER / Oxidoreductase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 Class A Carbapenemase in complex with Durlobactam
Authors: Dhankhar, K. / Hazra, S.
History
DepositionJun 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 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)61,6137
Polymers60,8072
Non-polymers8065
Water2,072115
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8244
Polymers30,4031
Non-polymers4213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area10890 Å2
MethodPISA
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7893
Polymers30,4031
Non-polymers3852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.355, 50.746, 129.9
Angle α, β, γ (deg.)90, 92.705, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 267 / Label seq-ID: 3 - 269

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein beta-lactamase / SME-1


Mass: 30403.297 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
#2: Chemical ChemComp-JXG / (2S,5R)-1-formyl-3-methyl-5-[(sulfooxy)amino]-1,2,5,6-tetrahydropyridine-2-carboxamide / ETX2514 bound form


Mass: 279.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.98 Å3/Da / Density % sol: 37.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 3350, 0.2M Lithium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→25.95 Å / Num. obs: 20681 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.994 / Rrim(I) all: 0.166 / Net I/σ(I): 7.5
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 15588 / CC1/2: 0.938

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25.386 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.885 / SU B: 20.972 / SU ML: 0.224 / Cross valid method: FREE R-VALUE / ESU R Free: 0.293
RfactorNum. reflection% reflection
Rfree0.2682 1028 4.974 %
Rwork0.1926 19638 -
all0.196 --
obs-20666 99.802 %
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: 14.082 Å2
Baniso -1Baniso -2Baniso -3
1-2.603 Å2-0 Å2-0.517 Å2
2---1.689 Å20 Å2
3----0.862 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 51 115 4286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124240
X-RAY DIFFRACTIONr_angle_refined_deg2.3971.8215712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0385532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.235534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.59810746
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.2510186
X-RAY DIFFRACTIONr_chiral_restr0.1490.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023198
X-RAY DIFFRACTIONr_nbd_refined0.230.22053
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22932
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3440.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.214
X-RAY DIFFRACTIONr_mcbond_it3.7311.2482134
X-RAY DIFFRACTIONr_mcangle_it5.8862.2432664
X-RAY DIFFRACTIONr_scbond_it4.9741.3892106
X-RAY DIFFRACTIONr_scangle_it7.3512.4833048
X-RAY DIFFRACTIONr_lrange_it29.46215.1276628
X-RAY DIFFRACTIONr_rigid_bond_restr5.47634240
X-RAY DIFFRACTIONr_ncsr_local_group_10.0990.058808
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.098580.05008
12AX-RAY DIFFRACTIONLocal ncs0.098580.05008
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
2.3-2.3590.328710.24414420.24815130.9150.961000.224
2.359-2.4230.309790.22913660.23314450.9360.9671000.211
2.423-2.4930.295670.19213740.19714410.9280.9771000.173
2.493-2.5690.269830.18713110.19313940.9530.9781000.168
2.569-2.6520.311670.212550.20513220.9410.9751000.178
2.652-2.7440.313590.2112690.21513280.9370.9731000.188
2.744-2.8470.307790.18711690.19412480.9520.9781000.167
2.847-2.9610.295530.19611890.212420.9480.9761000.173
2.961-3.0910.227460.16311050.16611510.9680.9841000.147
3.091-3.2390.252400.17410950.17711350.9510.9811000.157
3.239-3.4120.219710.199650.19310370.9740.97999.90360.173
3.412-3.6140.277410.1829740.18610170.9510.98299.80330.171
3.614-3.8580.238410.2089110.219520.9720.9731000.199
3.858-4.160.308430.1788400.1848880.9530.98299.43690.171
4.16-4.5440.242460.1897770.1928240.9620.97499.87860.181
4.544-5.0610.215500.1627070.1667590.9710.98699.73650.157
5.061-5.8050.24270.1716340.1746610.9790.9831000.161
5.805-7.0190.256290.25480.2035770.9770.9781000.19
7.019-9.5670.271190.1744340.1784540.9710.98399.77970.173
9.567-25.3860.204170.2192730.2182980.9820.97897.31540.221

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