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- PDB-3n6i: Crystal Structure of BlaC-E166A covalently bound with 6-aminopeni... -

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Basic information

Entry
Database: PDB / ID: 3n6i
TitleCrystal Structure of BlaC-E166A covalently bound with 6-aminopenicillian
ComponentsBeta-lactamase
KeywordsHydrolase/Antibiotic / penicillin binding protein / beta-lactam covalent adduct / Hydrolase-Antibiotic complex
Function / homology
Function and homology information


: / : / 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-XD1 / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTremblay, L.W. / Blanchard, J.S.
CitationJournal: To be Published
Title: The Structure Activity Relationship of BlaC with all classes of beta-lactams
Authors: Tremblay, L.W. / Blanchard, J.S.
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6234
Polymers28,2151
Non-polymers4083
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.855, 68.052, 75.469
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: 28214.689 Da / Num. of mol.: 1 / Mutation: E182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: blaA, blaC, MT2128, MTCY49.07c, Rv2068c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase
#2: Chemical ChemComp-XD1 / (2R,4S)-2-[(1R)-1-amino-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / 6-aminopenicillian, bound form


Mass: 218.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N2O3S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
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: 2009
RadiationMonochromator: Si(111) Channel Cut / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 17985 / Num. obs: 17985 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 7 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 3.4
Reflection shellResolution: 2→2.1 Å / Redundancy: 8 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2575 / % possible all: 100

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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
Starting model: PDB entry 3DWZ

3dwz


Resolution: 2→37.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.004 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.192 916 5.1 %RANDOM
Rwork0.15 ---
all0.152 17023 --
obs0.152 17939 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.38 Å2 / Biso mean: 7.444 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2→37.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 24 317 2325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222045
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9782795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4823.10387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6515302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7421519
X-RAY DIFFRACTIONr_chiral_restr0.0870.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211567
X-RAY DIFFRACTIONr_mcbond_it0.5421.51319
X-RAY DIFFRACTIONr_mcangle_it1.01222107
X-RAY DIFFRACTIONr_scbond_it1.8513726
X-RAY DIFFRACTIONr_scangle_it3.0944.5688
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 78 -
Rwork0.155 1235 -
all-1313 -
obs--100 %

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