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- PDB-2h5s: SA2-13 penam sulfone complexed to wt SHV-1 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 2h5s
TitleSA2-13 penam sulfone complexed to wt SHV-1 beta-lactamase
ComponentsSHV-1 beta-lactamase
KeywordsHYDROLASE / beta-lactamase inhibitor / 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-SA2 / Beta-lactamase SHV-1 / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
Authorsvan den Akker, F. / Padayatti, P.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Rational Design of a beta-Lactamase Inhibitor Achieved via Stabilization of the trans-Enamine Intermediate: 1.28 A Crystal Structure of wt SHV-1 Complex with a Penam Sulfone.
Authors: Padayatti, P.S. / Sheri, A. / Totir, M.A. / Helfand, M.S. / Carey, M.P. / Anderson, V.E. / Carey, P.R. / Bethel, C.R. / Bonomo, R.A. / Buynak, J.D. / van den Akker, F.
History
DepositionMay 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SHV-1 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2904
Polymers28,9071
Non-polymers1,3833
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.810, 55.220, 84.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsprotein is a monomer

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Components

#1: Protein SHV-1 beta-lactamase / Extended-spectrum beta-lactamase SHV-11 / SHV type extended spectrum beta-lactamase / Bla-SHV type 1


Mass: 28907.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: pBC SK(-) / Species (production host): Escherichia coli
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
Strain (production host): DH10B
References: UniProt: Q5PSW7, UniProt: P0AD64*PLUS, beta-lactamase
#2: Chemical ChemComp-SA2 / (3R)-4-[(4-CARBOXYBUTANOYL)OXY]-N-[(1E)-3-OXOPROP-1-EN-1-YL]-3-SULFINO-D-VALINE / 4-AZA-5-CARBOXY-6-SULFENATE-6-METHYL-8-OXA-9-OXO-TRIS-2-TRANS-DECENEDIOIC ACID


Mass: 365.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19NO9S
#3: Chemical ChemComp-MA4 / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE


Mass: 508.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H44O11
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30%PEG6000, 0.1M HEPES, 0.56 mM cymal-6, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: CCD / Detector: CCD / Date: Jul 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.28→23.22 Å / Num. all: 60720 / Num. obs: 59323 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 8.1 Å2 / Rsym value: 0.036 / Net I/σ(I): 41.5
Reflection shellResolution: 1.28→1.33 Å / Rsym value: 0.166 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RCJ

1rcj


Resolution: 1.28→23.22 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1288714.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.167 6018 10.1 %RANDOM
Rwork0.154 ---
obs0.154 59293 97.6 %-
all-60720 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.2015 Å2 / ksol: 0.36465 e/Å3
Displacement parametersBiso mean: 10.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2---1.18 Å20 Å2
3---0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.12 Å0.11 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.28→23.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 68 345 2480
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.28→1.36 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.195 945 9.9 %
Rwork0.17 8606 -
obs-8606 95.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3sa_par3.parnew_ligands5.top
X-RAY DIFFRACTION4new_cymal.parion.top
X-RAY DIFFRACTION5cis167new.par

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