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- PDB-3ndg: Crystal Structure of BlaC-E166A covalently bound with Methicillin -

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Basic information

Entry
Database: PDB / ID: 3ndg
TitleCrystal Structure of BlaC-E166A covalently bound with Methicillin
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-7EP / PHOSPHATE ION / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 7, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)28,7874
Polymers28,2151
Non-polymers5723
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.355, 67.908, 75.569
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) / 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-7EP / (2R,4S)-2-[(1R)-1-{[(2,6-dimethoxyphenyl)carbonyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / methicillin, bound form


Mass: 382.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N2O6S / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.19 %
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: 1.9→39.94 Å / Num. obs: 19843 / % possible obs: 95.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 15.323 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 5.2
Reflection shellResolution: 1.9→1.949 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2796 / % possible all: 95.36

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DWZ

3dwz


Resolution: 1.9→39.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.595 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1018 5.1 %RANDOM
Rwork0.153 ---
obs0.155 19808 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.09 Å2 / Biso mean: 17.13 Å2 / Biso min: 5.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 36 215 2235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222058
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9842813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1535264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61523.10387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70615302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6211519
X-RAY DIFFRACTIONr_chiral_restr0.0960.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021581
X-RAY DIFFRACTIONr_nbd_refined0.2130.2972
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21432
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2181
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.224
X-RAY DIFFRACTIONr_mcbond_it0.7921.51358
X-RAY DIFFRACTIONr_mcangle_it1.29422110
X-RAY DIFFRACTIONr_scbond_it2.1793797
X-RAY DIFFRACTIONr_scangle_it3.3644.5703
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 71 -
Rwork0.167 1348 -
all-1419 -
obs-2796 95.36 %

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