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- PDB-4q8i: Crystal Structure of beta-lactamase from M.tuberculosis covalentl... -

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Basic information

Entry
Database: PDB / ID: 4q8i
TitleCrystal Structure of beta-lactamase from M.tuberculosis covalently complexed with Tebipenem
ComponentsBeta-lactamase
Keywordshydrolase/antibiotic / betalactam / betalactamase / carbapenem / tebipenem / tebipenem pivoxil / 3-Layer Sandwich / DD-peptidase/beta-lactamase superfamily / hydrolase-antibiotic complex
Function / homology
Function and homology information


penicillinase activity / cephalosporinase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chem-TEB / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsHazra, S. / Blanchard, J.
CitationJournal: Biochemistry / Year: 2014
Title: Tebipenem, a new carbapenem antibiotic, is a slow substrate that inhibits the beta-lactamase from Mycobacterium tuberculosis.
Authors: Hazra, S. / Xu, H. / Blanchard, J.S.
History
DepositionApr 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,1666
Polymers28,4011
Non-polymers7655
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.925, 68.026, 75.554
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 / / Penicillinase


Mass: 28400.852 Da / Num. of mol.: 1 / Fragment: Beta-lactam destroying enzyme / Mutation: no mutation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: blaA, blaC, Rv2068c, MTCY49.07c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WKD3, 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
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, pH 7.5, 2M NH4H2PO4 Protein concentration 12 mgs/ml, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→41.65 Å / Num. all: 20497 / Num. obs: 20453
Reflection shellResolution: 1.9→41.65 Å / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HFX

4hfx


Resolution: 1.901→91.3595 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 2000 9.78 %
Rwork0.1611 --
obs0.1673 20453 97.91 %
all-20497 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→91.3595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 45 348 2381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062109
X-RAY DIFFRACTIONf_angle_d1.212885
X-RAY DIFFRACTIONf_dihedral_angle_d16.402793
X-RAY DIFFRACTIONf_chiral_restr0.068322
X-RAY DIFFRACTIONf_plane_restr0.004378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9006-1.94820.3931400.33231297X-RAY DIFFRACTION97
1.9482-2.00080.28091410.24711291X-RAY DIFFRACTION99
2.0008-2.05970.28911420.21061311X-RAY DIFFRACTION98
2.0597-2.12620.23491410.19321303X-RAY DIFFRACTION99
2.1262-2.20220.25621400.1811294X-RAY DIFFRACTION98
2.2022-2.29040.2881360.22281260X-RAY DIFFRACTION95
2.2904-2.39460.23381430.16641314X-RAY DIFFRACTION99
2.3946-2.52080.24791430.15631323X-RAY DIFFRACTION99
2.5208-2.67870.23141420.15631304X-RAY DIFFRACTION98
2.6787-2.88550.22351440.15411331X-RAY DIFFRACTION98
2.8855-3.17580.22051440.14131331X-RAY DIFFRACTION99
3.1758-3.63510.2011460.13061340X-RAY DIFFRACTION98
3.6351-4.57890.18031450.11561346X-RAY DIFFRACTION98
4.5789-41.66280.17781530.14711408X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 17.809 Å / Origin y: 6.936 Å / Origin z: 8.5607 Å
111213212223313233
T0.0791 Å2-0.0185 Å2-0.0111 Å2-0.0953 Å20.0092 Å2--0.1092 Å2
L0.6747 °2-0.0524 °2-0.1645 °2-0.6773 °2-0.0515 °2--1.5232 °2
S0.0034 Å °-0.0247 Å °-0.0329 Å °0.0402 Å °0.0076 Å °0.0199 Å °0.0575 Å °-0.0724 Å °-0.0102 Å °
Refinement TLS groupSelection details: all

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