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- PDB-8jk3: Crystal Structure of Bel-1 Extended Spectrum Beta-lactamase in He... -

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Basic information

Entry
Database: PDB / ID: 8jk3
TitleCrystal Structure of Bel-1 Extended Spectrum Beta-lactamase in Hexagonal Form
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / Apo
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
ACETATE ION / ISOPROPYL ALCOHOL / TRIETHYLENE GLYCOL / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDhankhar, K. / Hazra, S.
Funding support India, 1items
OrganizationGrant numberCountry
Other private India
CitationJournal: To Be Published
Title: Crystal Structure of Bel-1 ESBL in Hexagonal Form
Authors: Dhankhar, K. / Hazra, S.
History
DepositionMay 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,95616
Polymers58,2622
Non-polymers69514
Water10,953608
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.192, 121.192, 72.128
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase


Mass: 29130.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla(BEL1), blaBEL-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3SAW3, beta-lactamase

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Non-polymers , 7 types, 622 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M HEPES sodium pH 7.5, 30% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 1, 2022 / Details: X ray optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→29.126 Å / Num. obs: 96340 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.99 / CC star: 0.059 / Net I/σ(I): 18.4
Reflection shellResolution: 1.5→8.22 Å / Num. unique obs: 8448 / CC1/2: 0.418

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→29.126 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.271 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2088 4975 5.176 %
Rwork0.15 91144 -
all0.153 --
obs-96119 99.751 %
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: 20.523 Å2
Baniso -1Baniso -2Baniso -3
1--0.048 Å2-0.024 Å2-0 Å2
2---0.048 Å20 Å2
3---0.156 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 38 608 4709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164037
X-RAY DIFFRACTIONr_angle_refined_deg2.0091.6515676
X-RAY DIFFRACTIONr_angle_other_deg0.6751.5689280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1035540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.008530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63510708
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.77310180
X-RAY DIFFRACTIONr_chiral_restr0.1040.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02944
X-RAY DIFFRACTIONr_nbd_refined0.2390.2972
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.23910
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22131
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2411
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0530.21
X-RAY DIFFRACTIONr_metal_ion_refined0.4540.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2550.210
X-RAY DIFFRACTIONr_nbd_other0.2090.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2750.223
X-RAY DIFFRACTIONr_mcbond_it2.0182.0032152
X-RAY DIFFRACTIONr_mcbond_other2.0032.0022151
X-RAY DIFFRACTIONr_mcangle_it2.5263.5992694
X-RAY DIFFRACTIONr_mcangle_other2.5323.62695
X-RAY DIFFRACTIONr_scbond_it2.7022.392040
X-RAY DIFFRACTIONr_scbond_other2.7022.3912041
X-RAY DIFFRACTIONr_scangle_it3.4764.2142982
X-RAY DIFFRACTIONr_scangle_other3.4764.2152983
X-RAY DIFFRACTIONr_lrange_it4.40323.8095041
X-RAY DIFFRACTIONr_lrange_other4.39823.8045038
X-RAY DIFFRACTIONr_rigid_bond_restr5.9338229
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
1.5-1.5390.3413750.33966610.33970720.9180.91899.4910.341
1.539-1.5810.3413570.29565470.29869040.9150.9371000.297
1.581-1.6270.2943190.26463480.26666670.9390.951000.263
1.627-1.6760.2783610.21862220.22265830.9460.9671000.214
1.676-1.7310.2663360.19859920.20163290.950.97399.98420.191
1.731-1.7920.2293390.16457510.16860900.9670.9831000.154
1.792-1.8590.2492770.16756470.17159280.9610.98499.93250.149
1.859-1.9350.2342960.14953900.15456870.9680.98799.98240.127
1.935-2.020.2252730.13351940.13754690.9710.9999.96340.111
2.02-2.1190.1872270.12149720.12452050.980.99299.88470.103
2.119-2.2320.1962820.11946670.12349640.9760.99299.69780.098
2.232-2.3670.1922640.11744180.12246970.9780.99299.68060.095
2.367-2.5290.1782170.10242240.10644650.9820.99499.46250.085
2.529-2.730.1911850.11738980.1241130.9780.99299.27060.098
2.73-2.9880.1732240.12635690.12938140.9820.99199.44940.108
2.988-3.3360.1981750.12732450.13134430.9770.99199.3320.113
3.336-3.8440.1741540.14428890.14530540.9820.98999.63980.136
3.844-4.6880.1811440.12724590.1326200.980.99199.35110.124
4.688-6.5450.1951080.15719240.15920370.9810.98899.75450.153
6.545-29.1260.203620.1611270.16212020.9760.98698.91850.157

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