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- PDB-8iy4: Crystal structure of Class A beta-lactamase BlaA WT - complex wit... -

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Basic information

Entry
Database: PDB / ID: 8iy4
TitleCrystal structure of Class A beta-lactamase BlaA WT - complex with Meropenem
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / Beta-lactamase / Carbapenem / Antimicrobial resistance / Meropenem
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-MER / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBhattacharya, S. / Hazra, S.
Funding support India, 3items
OrganizationGrant numberCountry
Indian Council of Medical Research5/3/8/17/GIA-ITR India
Indian Council of Medical ResearchBIC/12(15)/2014, India
Science and Engineering Research Board (SERB)YSS/2014/000492 India
CitationJournal: To be published
Title: Crystal structure of Class A beta-lactamase BlaA WT - complex with Meropenem
Authors: Bhattacharya, S. / Hazra, S.
History
DepositionApr 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4473
Polymers31,9671
Non-polymers4802
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-4 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.774, 72.619, 43.707
Angle α, β, γ (deg.)90.000, 94.953, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

21A-525-

HOH

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Components

#1: Protein Beta-lactamase / Penicillinase


Mass: 31966.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: blaA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01166, beta-lactamase
#2: Chemical ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.29 Å3/Da / Density % sol: 46.37 % / Description: Single crystal with cubic in nature
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic
PH range: 7.0-9.0

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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 5, 2022 / Details: X ray optics
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→24.53 Å / Num. obs: 19371 / % possible obs: 99.9 % / Redundancy: 10.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.091 / Rrim(I) all: 0.22 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.05-24.526.80.0882180.9940.0490.101
2-2.0510.40.65513980.8890.3110.728

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
CrysalisProdata collection
Cootmodel building
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.53 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.892 / SU B: 5.297 / SU ML: 0.147 / Cross valid method: FREE R-VALUE / ESU R: 0.197 / ESU R Free: 0.186
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2641 940 4.853 %
Rwork0.2023 18429 -
all0.205 --
obs-19369 99.871 %
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: 20.949 Å2
Baniso -1Baniso -2Baniso -3
1-2.416 Å2-0 Å20.978 Å2
2---1.22 Å20 Å2
3----1.345 Å2
Refinement stepCycle: LAST / Resolution: 2→24.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 31 180 2203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122059
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161992
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.6522799
X-RAY DIFFRACTIONr_angle_other_deg0.4711.574563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8325259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.252521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62710342
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.1711088
X-RAY DIFFRACTIONr_chiral_restr0.0650.2326
X-RAY DIFFRACTIONr_chiral_restr_other0.0170.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022446
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02474
X-RAY DIFFRACTIONr_nbd_refined0.2110.2488
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21968
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21023
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21123
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2570.2134
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.236
X-RAY DIFFRACTIONr_nbd_other0.1780.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2240.236
X-RAY DIFFRACTIONr_mcbond_it1.642.051039
X-RAY DIFFRACTIONr_mcbond_other1.6392.051039
X-RAY DIFFRACTIONr_mcangle_it2.5543.6731297
X-RAY DIFFRACTIONr_mcangle_other2.5533.6761298
X-RAY DIFFRACTIONr_scbond_it2.322.3921020
X-RAY DIFFRACTIONr_scbond_other2.2952.3781017
X-RAY DIFFRACTIONr_scangle_it3.6744.271502
X-RAY DIFFRACTIONr_scangle_other3.634.2381497
X-RAY DIFFRACTIONr_lrange_it6.75625.1262435
X-RAY DIFFRACTIONr_lrange_other6.42524.2612382
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
2-2.0520.363730.23713160.24413890.9050.9581000.226
2.052-2.1070.236720.23513220.23513940.9590.9581000.223
2.107-2.1680.304650.22113050.22513700.9470.9641000.209
2.168-2.2340.28760.22812230.23112990.9520.9631000.214
2.234-2.3070.326590.21311980.21812570.9290.9661000.201
2.307-2.3870.27690.21611350.21912040.9480.9661000.202
2.387-2.4760.298520.20111380.20511900.9440.9721000.189
2.476-2.5760.307510.18611150.19111660.9510.9761000.175
2.576-2.690.265440.19210530.19510970.960.9741000.182
2.69-2.8190.263530.1979890.20110420.9570.9721000.19
2.819-2.9690.25510.2069430.2089950.9520.97199.89950.199
2.969-3.1470.302450.2099040.2139490.9380.9691000.203
3.147-3.360.222340.28650.2018990.9670.9721000.198
3.36-3.6240.269400.1987860.2028260.9410.9741000.199
3.624-3.9610.276260.1917360.1947660.9480.97699.47780.197
3.961-4.4140.19340.1856690.1857040.9730.97599.8580.19
4.414-5.0690.241410.1765720.186130.9660.981000.186
5.069-6.1430.253370.2134970.2165360.9610.97399.62690.219
6.143-8.4280.257150.1984060.24220.9730.97299.7630.209
8.428-24.530.09230.1832570.1822650.9960.97598.11320.197

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