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- PDB-1q2p: SHV-1 class A beta-lactamase complexed with penem WAY185229 -

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Basic information

Entry
Database: PDB / ID: 1q2p
TitleSHV-1 class A beta-lactamase complexed with penem WAY185229
Componentsbeta-lactamase SHV-1
KeywordsHYDROLASE / inhibition / beta-lactam antibiotics / drug design
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / 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-WY2 / Beta-lactamase SHV-1 / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNukaga, M. / Venkatesan, A.M. / Mansour, T.S. / Hujer, A. / Bonomo, R.A. / Knox, J.R.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Structure-activity relationship of 6-methylidene penems bearing tricyclic heterocycles as broad-spectrum beta-lactamase inhibitors: crystallographic structures show unexpected binding of 1,4- ...Title: Structure-activity relationship of 6-methylidene penems bearing tricyclic heterocycles as broad-spectrum beta-lactamase inhibitors: crystallographic structures show unexpected binding of 1,4-thiazepine intermediates
Authors: Venkatesan, A.M. / Gu, Y. / Dos Santos, O. / Abe, T. / Agarwal, A. / Yang, Y. / Petersen, P.J. / Weiss, W.J. / Mansour, T.S. / Nukaga, M. / Hujer, A. / Bonomo, R.A. / Knox, J.R.
History
DepositionJul 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
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_conn / 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_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)30,2884
Polymers28,9071
Non-polymers1,3813
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.532, 55.105, 84.154
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein beta-lactamase SHV-1 / E.C.3.5.2.6 / PIT-2 / extended-spectrum beta-lactamase SHV-1


Mass: 28907.018 Da / Num. of mol.: 1 / Fragment: PENICILLINASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: BLA / Plasmid: PBCSK / Species (production host): Escherichia coli
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-WY2 / (6,7-DIHYDRO-5H-CYCLOPENTA[D]IMIDAZO[2,1-B]THIAZOL-2-YL]-4,7-DIHYDRO[1,4]THIAZEPINE-3,6-DICARBOXYLIC ACID


Mass: 363.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13N3O4S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 6000, HEPES, CYMAL-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Dec 23, 2002 / Details: Franks Mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 15709 / Num. obs: 15709 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 6.8 Å2 / Rsym value: 0.059 / Net I/σ(I): 18.3
Reflection shellResolution: 2→2.13 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 5 / Num. unique all: 2218 / Rsym value: 0.152 / % possible all: 84.4

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SHV

1shv


Resolution: 2→27.72 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.189 759 4.9 %RANDOM
Rwork0.166 ---
all0.163 15525 --
obs0.163 15525 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 89.1837 Å2 / ksol: 0.5094 e/Å3
Displacement parametersBiso mean: 12.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å20 Å20 Å2
2---1.96 Å20 Å2
3----1.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2→27.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 68 193 2320
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.512
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.852.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.222 89 4.2 %
Rwork0.172 2042 -
obs-2131 81.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARM.MA1PARM.TOP
X-RAY DIFFRACTION4WY2.PARWY2.TOP

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