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- PDB-1ong: SHV-1 beta-lactamase with a penem inhibitor -

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Basic information

Entry
Database: PDB / ID: 1ong
TitleSHV-1 beta-lactamase with a penem inhibitor
ComponentsBETA-LACTAMASE SHV-1
KeywordsHYDROLASE / BETA-LACTAM HYDROLASE / PENICILLINASE / DETERGENT BINDING / DRUG DESIGN
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
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
CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE / Chem-WY4 / Beta-lactamase SHV-1 / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsNukaga, M. / Mayama, K. / Bonomo, R.A. / Knox, J.R.
CitationJournal: Biochemistry / Year: 2003
Title: Inhibition of Class A and Class C Beta-Lactamases by Penems: Crystallographic Structures of a Novel 1,4-Thiazepine Intermediate
Authors: Nukaga, M. / Abe, T. / Venkatesan, A.M. / Mansour, T.S. / Bonomo, R.A. / Knox, J.R.
History
DepositionFeb 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 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 SHV-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2324
Polymers28,9071
Non-polymers1,3253
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.555, 55.183, 85.315
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 SHV-1 / PIT-2 / PENICILLINASE


Mass: 28907.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: 15571 / Gene: BLA / Plasmid: PBCSK / Species (production host): Escherichia coli / Gene (production host): BLA
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
Strain (production host): DH10B
References: UniProt: P14557, UniProt: P0AD64*PLUS, beta-lactamase
#2: Chemical ChemComp-MA4 / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE


Mass: 508.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H44O11
#3: Chemical ChemComp-WY4 / 7-(5,6-DIHYDRO-8H-IMIDAZO[2,1-C][1,4]OXAZIN-2-YL)-6-FORMYL-2,7-DIHYDRO- [1,4]THIAZEPINE-3-CARBOXYLIC ACID


Mass: 307.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13N3O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% PEG-6000, 50 mM HEPES, 0.56 mM CYMAL-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 mg/mlprotein1drop
20.6 mMCymal-61drop
315 %PEG60001drop
450 mMHEPES1droppH7.0
530 %PEG1reservoir
6100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9349 / Wavelength: 0.9349 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9349 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 87983 / % possible obs: 92.6 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.5
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3.3 / Num. unique all: 6959 / % possible all: 74.2
Reflection
*PLUS
Num. measured all: 1019910
Reflection shell
*PLUS
% possible obs: 74.2 % / Num. unique obs: 6959 / Num. measured obs: 30641 / Rmerge(I) obs: 0.374

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHV

1shv


Resolution: 1.1→20 Å / Num. parameters: 22711 / Num. restraintsaints: 28932 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 3560 4 %RANDOM
Rwork0.1413 ---
all0.1414 88320 --
obs0.1414 88320 92.5 %-
Refine analyzeNum. disordered residues: 47 / Occupancy sum hydrogen: 2002.75 / Occupancy sum non hydrogen: 2344.9
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 77 296 2513
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0351
X-RAY DIFFRACTIONs_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.028
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0.1
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.186 / Rfactor Rwork: 0.141
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.035
X-RAY DIFFRACTIONs_chiral_restr0.081

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