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- PDB-3ny4: Crystal Structure of BlaC-K73A bound with Cefamandole -

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Basic information

Entry
Database: PDB / ID: 3ny4
TitleCrystal Structure of BlaC-K73A bound with Cefamandole
ComponentsBeta-lactamase
KeywordsHYDROLASE/ANTIBIOTIC / penicillin binding protein / beta-lactam complex / 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-SMX / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsTremblay, L.W. / Blanchard, J.S.
CitationJournal: Biochemistry / Year: 2010
Title: Structures of the Michaelis Complex (1.2 A) and the Covalent Acyl Intermediate (2.0 A) of Cefamandole Bound in the Active Sites of the Mycobacterium tuberculosis beta-Lactamase K73A and E166A Mutants.
Authors: Tremblay, L.W. / Xu, H. / Blanchard, J.S.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Non-polymer description
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)30,6227
Polymers28,2151
Non-polymers2,4076
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.804, 67.915, 75.524
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase / Penicillinase


Mass: 28214.623 Da / Num. of mol.: 1 / Mutation: K87A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaA, blaC, Rv2068c, MT2128, MTCY49.07c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-SMX / (6R,7R)-7-{[(2R)-2-hydroxy-2-phenylacetyl]amino}-3-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid / CEFAMANDOLE, free form


Mass: 462.503 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H18N6O5S2 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 45.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 2 M NH4H2PO4, pH 7.5, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 30, 2010
RadiationMonochromator: Si(111) Channel Cut / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. all: 76776 / Num. obs: 76623 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 10.218 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 32.5
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3769 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→40.16 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.119 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1785 3848 5 %RANDOM
Rwork0.1573 ---
obs0.1584 76546 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.8 Å2 / Biso mean: 14.7059 Å2 / Biso min: 5.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0 Å2
2--0.08 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.22→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 160 237 2381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222239
X-RAY DIFFRACTIONr_angle_refined_deg1.9712.0573076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.015266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44323.18288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.91315301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0261519
X-RAY DIFFRACTIONr_chiral_restr0.1770.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0221761
X-RAY DIFFRACTIONr_mcbond_it1.1861.51357
X-RAY DIFFRACTIONr_mcangle_it1.98922179
X-RAY DIFFRACTIONr_scbond_it2.7633882
X-RAY DIFFRACTIONr_scangle_it4.2984.5885
X-RAY DIFFRACTIONr_rigid_bond_restr1.15732239
LS refinement shellResolution: 1.22→1.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 275 -
Rwork0.301 5267 -
all-5542 -
obs--99.11 %

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