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- PDB-9qi3: Crystal structure of I105Y/S130G double mutant of BlaC from Mycob... -

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Basic information

Entry
Database: PDB / ID: 9qi3
TitleCrystal structure of I105Y/S130G double mutant of BlaC from Mycobacterium tuberculosis
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / BlaC
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region
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
ACETATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsChikunova, A. / Radojkovic, M. / Ubbink, M.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)OCENW.KLEIN.264 Netherlands
CitationJournal: Protein Sci. / Year: 2025
Title: Phosphate ions modulate enzyme activity and epistatic effects in two clavulanic acid-resistant beta-lactamase mutants.
Authors: Radojkovic, M. / Koene, S.F. / Chikunova, A. / Florea, B.I. / Natarajan, S.V. / Boyle, A.L. / Ubbink, M.
History
DepositionMar 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 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)56,9756
Polymers56,7002
Non-polymers2764
Water12,502694
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4092
Polymers28,3501
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5664
Polymers28,3501
Non-polymers2173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.440, 41.425, 269.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase / Ambler class A beta-lactamase


Mass: 28349.766 Da / Num. of mol.: 2 / Mutation: I105Y, S130G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, blaA, BQ2027_MB2094C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A5I7, beta-lactamase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.94 Å3/Da / Density % sol: 36.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.015M Zn Chloride, 0.13M Na Acetate, 22%v/v PEGSM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.3→135.18 Å / Num. obs: 109981 / % possible obs: 99.7 % / Redundancy: 1.9 % / CC1/2: 0.972 / Net I/σ(I): 12.2
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 5438 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→135.18 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.826 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17407 5438 4.9 %RANDOM
Rwork0.14041 ---
obs0.14206 104543 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.381 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0 Å2
2--0.12 Å2-0 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.3→135.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 15 694 4699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124447
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164171
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.8196100
X-RAY DIFFRACTIONr_angle_other_deg0.6531.7599564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6485594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.414541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.09910669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025554
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021030
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8990.6582315
X-RAY DIFFRACTIONr_mcbond_other1.8760.6572313
X-RAY DIFFRACTIONr_mcangle_it2.8521.1832928
X-RAY DIFFRACTIONr_mcangle_other2.8531.1832929
X-RAY DIFFRACTIONr_scbond_it2.760.7862132
X-RAY DIFFRACTIONr_scbond_other2.7590.7872133
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0471.393173
X-RAY DIFFRACTIONr_long_range_B_refined11.17812.685281
X-RAY DIFFRACTIONr_long_range_B_other10.0219.935060
X-RAY DIFFRACTIONr_rigid_bond_restr3.03938618
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 409 -
Rwork0.197 7621 -
obs--99.94 %
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)
10.91360.0987-0.16040.6854-0.10580.6385-0.0282-0.0749-0.00820.04240.02930.03780.0170.0065-0.00110.01160.01160.00350.01460.00330.00231.6781-10.4887-51.4302
20.8865-0.086-0.39230.60690.38611.0137-0.00810.00750.0293-0.05850.0398-0.0254-0.00490.0308-0.03160.04190.00340.00280.0332-0.00630.0095-10.1228-21.1228-17.1901
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 293
2X-RAY DIFFRACTION2B27 - 293

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