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- PDB-2wzz: AMP-C BETA-LACTAMASE (PSEUDOMONAS AERUGINOSA)IN COMPLEX WITH comp... -

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Basic information

Entry
Database: PDB / ID: 2wzz
TitleAMP-C BETA-LACTAMASE (PSEUDOMONAS AERUGINOSA)IN COMPLEX WITH compound M-03
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / INHIBITOR / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ZX1 / Beta-lactamase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.57 Å
AuthorsFitzgerald, P.M.D. / Sharma, N. / Lu, J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: Side Chain Sar of Bicyclic Beta-Lactamase Inhibitors (Blis). 1. Discovery of a Class C Bli for Combination with Imipinem.
Authors: Blizzard, T.A. / Chen, H. / Kim, S. / Wu, J. / Young, K. / Park, Y. / Ogawa, A. / Raghoobar, S. / Painter, R.E. / Hairston, N. / Lee, S.H. / Misura, A. / Felcetto, T. / Fitzgerald, P.M.D. / ...Authors: Blizzard, T.A. / Chen, H. / Kim, S. / Wu, J. / Young, K. / Park, Y. / Ogawa, A. / Raghoobar, S. / Painter, R.E. / Hairston, N. / Lee, S.H. / Misura, A. / Felcetto, T. / Fitzgerald, P.M.D. / Sharma, N. / Lu, J. / Ha, S. / Hickey, E. / Hermes, J. / Hammond, M.L.
History
DepositionDec 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1103
Polymers40,7241
Non-polymers3862
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.791, 72.575, 106.271
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 / AMP-C BETA-LACTAMASE / CEPHALOSPORINASE


Mass: 40723.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24735, beta-lactamase
#2: Chemical ChemComp-ZX1 / (3R)-1-[(4R)-AZEPAN-4-YLCARBAMOYL]-3-(SULFOAMINO)-L-PROLINE


Mass: 350.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N4O6S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.54 % / Description: NONE

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 48596 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.57→59.93 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.314 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19659 2456 5.1 %RANDOM
Rwork0.18058 ---
obs0.18139 46064 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.233 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.57→59.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 23 290 3075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222892
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9813948
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63523.846130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06315439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0481520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212267
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.541.51816
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03322900
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8431076
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0694.51048
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.574→1.615 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 178 -
Rwork0.234 3062 -
obs--90.91 %

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