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- PDB-3nbl: Crystal Structure of BlaC-E166A covalently bound with Cefuroxime -

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Basic information

Entry
Database: PDB / ID: 3nbl
TitleCrystal Structure of BlaC-E166A covalently bound with Cefuroxime
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
Chem-DXF / 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: BlaC-E166A covalently bound with cephalosporins and penicillins
Authors: Tremblay, L.W. / Blanchard, J.S.
History
DepositionJun 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Non-polymer description / Structure summary
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)28,6412
Polymers28,2151
Non-polymers4261
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.383, 68.102, 75.652
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-DXF / (2R)-5-[(carbamoyloxy)methyl]-2-[(1R)-1-{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}-2-oxoethyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / Cefuroxime, bound form


Mass: 426.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N4O8S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C11
SYNCHROTRONNSLS X29A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCD2009
ADSC QUANTUM 2102CCD2009
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si(111) Channel CutSINGLE WAVELENGTHx-ray1
2Si(111) Channel CutSINGLE WAVELENGTHx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 2→50 Å / Num. all: 17823 / Num. obs: 17823 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.32 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.053 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 4.1 / Num. unique all: 866 / % possible all: 98.6

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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→35.35 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.457 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 902 5.1 %RANDOM
Rwork0.181 ---
obs0.183 17774 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 44.3 Å2 / Biso mean: 10.681 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 29 191 2168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222016
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.982751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.795259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3723.09584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.30815294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8731518
X-RAY DIFFRACTIONr_chiral_restr0.0710.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211558
X-RAY DIFFRACTIONr_mcbond_it0.4721.51299
X-RAY DIFFRACTIONr_mcangle_it0.89322075
X-RAY DIFFRACTIONr_scbond_it1.5643717
X-RAY DIFFRACTIONr_scangle_it2.6614.5676
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 71 -
Rwork0.19 1208 -
all-1279 -
obs--98.61 %

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