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- PDB-9xfy: Crystal structure of Class A beta-lactamase BlaA in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9xfy
TitleCrystal structure of Class A beta-lactamase BlaA in complex with ertapenem (imine form)
ComponentsBeta-lactamase
KeywordsHYDROLASE / Imine tautomer / Carbapenemase / Acyl enzyme 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 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-2RG / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBhattacharya, S. / Dhankhar, K. / Hazra, S.
Funding support India, 2items
OrganizationGrant numberCountry
Indian Council of Medical Research India
Board of Research in Nuclear Sciences (BRNS) India
CitationJournal: To Be Published
Title: Crystal structure of Class A beta-lactamase BlaA in complex with ertapenem (imine form)
Authors: Bhattacharya, S. / Dhankhar, K. / Hazra, S.
History
DepositionOct 29, 2025Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 12, 2025ID: 8IXX
Revision 1.0Nov 12, 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)32,7295
Polymers31,9671
Non-polymers7624
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-15 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.743, 72.818, 43.7
Angle α, β, γ (deg.)90, 95.776, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

21A-559-

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-2RG / (2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / ERTAPENEM, bound form POST-ISOMERIZED


Mass: 477.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N3O7S / 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.: 212 / 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: 45.85 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.7→24.663 Å / Num. obs: 31443 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.078 / Rrim(I) all: 0.154 / Net I/σ(I): 7.4
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.591 / Num. unique obs: 6673 / CC1/2: 0.809 / Rpim(I) all: 0.332 / Rrim(I) all: 0.682

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E2E

5e2e


Resolution: 1.7→24.663 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.508 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.111 / ESU R Free: 0.11
RfactorNum. reflection% reflection
Rfree0.2298 1608 5.114 %
Rwork0.1936 29834 -
all0.196 --
obs-31442 99.791 %
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: 21.318 Å2
Baniso -1Baniso -2Baniso -3
1-2.066 Å2-0 Å20.45 Å2
2---1.124 Å2-0 Å2
3----1.012 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 48 212 2264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122088
X-RAY DIFFRACTIONr_angle_refined_deg2.0461.8142840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.633521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96110342
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.0081088
X-RAY DIFFRACTIONr_chiral_restr0.1710.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021567
X-RAY DIFFRACTIONr_nbd_refined0.2270.21069
X-RAY DIFFRACTIONr_nbtor_refined0.310.21460
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2161
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1380.227
X-RAY DIFFRACTIONr_mcbond_it1.7111.7451050
X-RAY DIFFRACTIONr_mcangle_it2.3963.1221309
X-RAY DIFFRACTIONr_scbond_it3.1312.2221038
X-RAY DIFFRACTIONr_scangle_it4.7413.9251531
X-RAY DIFFRACTIONr_lrange_it8.98125.6033379
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
1.7-1.7440.3131140.29321960.29423120.9320.93799.91350.294
1.744-1.7920.261210.26420990.26322200.9540.951000.261
1.792-1.8430.2531060.22921190.23122250.9580.9631000.223
1.843-1.90.2571160.20220220.20521380.9640.9711000.196
1.9-1.9610.231080.19619270.19820350.9590.9721000.19
1.961-2.030.239900.19419130.19620030.9640.9751000.187
2.03-2.1060.2271050.19218300.19419350.9640.9771000.188
2.106-2.1910.241970.19317620.19518590.9640.9771000.189
2.191-2.2880.225840.18416850.18617690.9720.9781000.181
2.288-2.3990.231970.17316060.17717030.9650.981000.174
2.399-2.5270.184760.17115560.17116340.9750.9899.87760.173
2.527-2.6780.239730.18814580.19115320.9650.97699.93470.194
2.678-2.8610.267680.19413660.19714340.9560.9751000.202
2.861-3.0870.213750.19812840.19913600.9710.97499.92650.207
3.087-3.3760.255700.20111820.20412570.9490.97299.60220.216
3.376-3.7660.24550.17810580.18111200.9640.97899.3750.2
3.766-4.3320.201520.1739480.17410040.9730.97999.60160.19
4.332-5.2650.183510.1648020.1668630.9790.98298.84120.185
5.265-7.2810.207340.2116440.216850.9680.97498.97810.233
7.281-24.6630.251160.2093770.214090.9750.97396.0880.243

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