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- PDB-8ix8: Crystal structure of Class A beta-lactamase BlaA WT - complex wit... -

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Basic information

Entry
Database: PDB / ID: 8ix8
TitleCrystal structure of Class A beta-lactamase BlaA WT - complex with Tebipenem
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / Beta-lactamase / Hydrolase / Antimicrobial resistance / Tebipenem
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 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
PHOSPHATE ION / Chem-TEB / Beta-lactamase
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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 Tebipenem
Authors: Bhattacharya, S. / Hazra, S.
History
DepositionMar 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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)32,6375
Polymers31,9671
Non-polymers6704
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-1 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.342, 72.182, 43.543
Angle α, β, γ (deg.)90.000, 96.087, 90.000
Int Tables number5
Space group name H-MC121

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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-TEB / (4R,5S)-3-(1-(4,5-dihydrothiazol-2-yl)azetidin-3-ylthio)-5-((2S,3R)-3-hydroxy-1-oxobutan-2-yl)-4-methyl-4,5- dihydro-1H-pyrrole-2-carboxylic acid / Tebipenem (open form)


Mass: 385.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H23N3O4S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.25 Å3/Da / Density % sol: 45.39 % / Description: Crystal morphology is 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: Nov 23, 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: 1.5→27.92 Å / Num. obs: 44966 / % possible obs: 99.9 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.038 / Rrim(I) all: 0.111 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.53-27.92140.0472840.9990.0160.05
1.5-1.539.21.00322270.6570.5121.13

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Cootmodel building
Aimlessdata scaling
CrysalisProdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→24.597 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.343 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2013 2244 4.992 %
Rwork0.1673 42707 -
all0.169 --
obs-44951 99.896 %
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: 14.192 Å2
Baniso -1Baniso -2Baniso -3
1-1.177 Å2-0 Å20.065 Å2
2---0.555 Å20 Å2
3----0.622 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 40 279 2336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122093
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162016
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.6532848
X-RAY DIFFRACTIONr_angle_other_deg0.61.5714621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.345263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.245523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89810344
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.0731088
X-RAY DIFFRACTIONr_chiral_restr0.0930.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022472
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02476
X-RAY DIFFRACTIONr_nbd_refined0.2290.2493
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.21904
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21056
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21160
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2170
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3880.231
X-RAY DIFFRACTIONr_nbd_other0.2590.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.241
X-RAY DIFFRACTIONr_mcbond_it1.4631.2461055
X-RAY DIFFRACTIONr_mcbond_other1.4591.2461055
X-RAY DIFFRACTIONr_mcangle_it2.1682.2331317
X-RAY DIFFRACTIONr_mcangle_other2.1672.2361318
X-RAY DIFFRACTIONr_scbond_it3.2071.6951038
X-RAY DIFFRACTIONr_scbond_other3.0291.6441027
X-RAY DIFFRACTIONr_scangle_it4.8452.9521529
X-RAY DIFFRACTIONr_scangle_other4.6512.8531512
X-RAY DIFFRACTIONr_lrange_it6.88120.0682515
X-RAY DIFFRACTIONr_lrange_other6.55916.7912425
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
1.5-1.5390.2431960.24131230.24233210.9570.95799.93980.231
1.539-1.5810.2611470.22330360.22431860.9520.96599.90580.208
1.581-1.6260.2311600.2129810.21131440.9630.96999.90460.195
1.626-1.6760.2491580.229090.20330670.9560.9731000.183
1.676-1.7310.2191390.18727790.18929190.9660.97799.96570.171
1.731-1.7910.2191280.17827340.1828660.9660.97899.86040.161
1.791-1.8590.1871350.16325950.16427320.9790.98299.92680.148
1.859-1.9340.2041270.16925670.17126940.9730.9811000.155
1.934-2.020.2091210.16724120.16925330.9720.9811000.156
2.02-2.1170.1911410.15222820.15424230.9760.9851000.144
2.117-2.2310.1911090.15122220.15323320.9790.98599.95710.146
2.231-2.3650.1931320.14220570.14521890.9760.9871000.139
2.365-2.5270.1791100.14219700.14420820.980.98799.90390.143
2.527-2.7270.188760.15618440.15719210.9780.98499.94790.157
2.727-2.9830.237930.16216680.16617660.9670.98399.71690.166
2.983-3.3290.165860.15515410.15516300.9790.98599.8160.164
3.329-3.8330.194640.14913630.15114270.9820.9861000.164
3.833-4.6660.152550.14811610.14912190.9830.98699.75390.166
4.666-6.4830.221430.1939160.1949630.9770.97999.58460.217
6.483-24.5970.227240.1965460.1985730.9680.97399.47640.223

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