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- PDB-8iwv: Crystal structure of BlaA-1 APO -

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Basic information

Entry
Database: PDB / ID: 8iwv
TitleCrystal structure of BlaA-1 APO
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / Beta-lactamase / Hydrolase
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 / Beta-lactamase
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 BlaA-1 APO
Authors: Bhattacharya, S. / Hazra, S.
History
DepositionMar 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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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)32,1573
Polymers31,9671
Non-polymers1902
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-7 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.450, 72.647, 43.887
Angle α, β, γ (deg.)90.000, 94.302, 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 / Plasmid: pET28a / Details (production host): pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01166, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24631381 Å3/Da / Density % sol: 45.2776413 %
Description: Crystal quality is good, generally cubic in shape.
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
Ambient temp details: Oxford cryosystem, continuous flow of nitrogen gas
Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541838 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 29, 2022 / Details: X ray optics
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541838 Å / Relative weight: 1
ReflectionResolution: 2.4→28.16 Å / Num. obs: 11023 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.072 / Rrim(I) all: 0.15 / Net I/σ(I): 9.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.284 / Num. unique obs: 11023 / CC1/2: 0.973 / Rpim(I) all: 0.155 / Rrim(I) all: 0.326 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
CrysalisProdata collection
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→28.16 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.732 / SU ML: 0.195 / Cross valid method: FREE R-VALUE / ESU R: 0.451 / ESU R Free: 0.264
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.235 567 5.144 %
Rwork0.1574 10455 -
all0.161 --
obs-11022 99.828 %
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: 22.945 Å2
Baniso -1Baniso -2Baniso -3
1-4.457 Å20 Å21.879 Å2
2---2.379 Å20 Å2
3----2.335 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 10 210 2212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122035
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161966
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.6442766
X-RAY DIFFRACTIONr_angle_other_deg0.4671.574504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.902516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2710342
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.1041088
X-RAY DIFFRACTIONr_chiral_restr0.0620.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
X-RAY DIFFRACTIONr_nbd_refined0.2210.2471
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21915
X-RAY DIFFRACTIONr_nbtor_refined0.180.21021
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2148
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0480.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.217
X-RAY DIFFRACTIONr_nbd_other0.2030.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2550.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0720.22
X-RAY DIFFRACTIONr_mcbond_it1.8172.3351039
X-RAY DIFFRACTIONr_mcbond_other1.8172.3351039
X-RAY DIFFRACTIONr_mcangle_it2.8174.1871297
X-RAY DIFFRACTIONr_mcangle_other2.8164.191298
X-RAY DIFFRACTIONr_scbond_it2.6522.665996
X-RAY DIFFRACTIONr_scbond_other2.5412.644989
X-RAY DIFFRACTIONr_scangle_it4.3774.7521469
X-RAY DIFFRACTIONr_scangle_other4.2014.7081458
X-RAY DIFFRACTIONr_lrange_it7.44826.3922414
X-RAY DIFFRACTIONr_lrange_other7.14825.282364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.363370.217753X-RAY DIFFRACTION99.8736
2.462-2.5290.247320.195752X-RAY DIFFRACTION100
2.49-8.980.31250.149143X-RAY DIFFRACTION96.1039
2.529-2.6020.311420.202740X-RAY DIFFRACTION100
2.602-2.6810.238460.183684X-RAY DIFFRACTION100
2.681-2.7680.306250.191700X-RAY DIFFRACTION100
2.768-2.8640.328420.179653X-RAY DIFFRACTION100
2.864-2.9710.291300.165644X-RAY DIFFRACTION100
2.971-3.0910.276390.166617X-RAY DIFFRACTION100
3.091-3.2270.184300.168584X-RAY DIFFRACTION100
3.227-3.3820.315220.163593X-RAY DIFFRACTION100
3.382-3.5620.228300.151529X-RAY DIFFRACTION99.8214
3.562-3.7740.154290.148503X-RAY DIFFRACTION100
3.774-4.030.213270.129482X-RAY DIFFRACTION100
4.03-4.3450.177200.118453X-RAY DIFFRACTION99.5789
4.345-4.7490.205200.12413X-RAY DIFFRACTION99.7696
4.749-5.2910.194300.133375X-RAY DIFFRACTION100
5.291-6.0730.229290.163323X-RAY DIFFRACTION100
6.073-7.3530.246190.146286X-RAY DIFFRACTION100
7.353-10.0620.1130.098228X-RAY DIFFRACTION100

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