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- PDB-2a3u: Crystal structure of sulbactam bound to E166A variant of SHV-1 be... -

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Basic information

Entry
Database: PDB / ID: 2a3u
TitleCrystal structure of sulbactam bound to E166A variant of SHV-1 beta-lactamase
ComponentsBeta-lactamase SHV-1
KeywordsHYDROLASE / BETA-LACTAMASE / BETA-LACTAM HYDROLASE / PENICILLINASE / DETERGENT BINDING / INHIBITOR DESIGN / COVALENT INTERMEDIATE
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 / TRANS-ENAMINE INTERMEDIATE OF SULBACTAM / Beta-lactamase SHV-1 / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsPadayatti, P.S. / Helfand, M.S. / Totir, M.A. / Carey, M.P. / Carey, P.R. / Bonomo, R.A. / van den Akker, F.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: High Resolution Crystal Structures of the trans-Enamine Intermediates Formed by Sulbactam and Clavulanic Acid and E166A SHV-1 {beta}-Lactamase.
Authors: Padayatti, P.S. / Helfand, M.S. / Totir, M.A. / Carey, M.P. / Carey, P.R. / Bonomo, R.A. / van den Akker, F.
History
DepositionJun 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN ONLY PART OF THE MOLECULE EPE IS VISIBLE AND MODELED. THE MOLECULE MA4 HAS ONE MOLECULE ...HETEROGEN ONLY PART OF THE MOLECULE EPE IS VISIBLE AND MODELED. THE MOLECULE MA4 HAS ONE MOLECULE THAT IS PRESENT IN ITS ENTIRITY, THE SECOND HAS A SMALLER PART THAT IS VISIBLE.THE COMPOUND TSL IS COVALENTLY REACTED WITH THE ACTIVE SITE SER70

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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)30,9105
Polymers29,4201
Non-polymers1,4914
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.510, 55.310, 83.730
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


Mass: 29419.725 Da / Num. of mol.: 1 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, shv1 / Production host: Escherichia coli (E. coli)
References: UniProt: P14557, UniProt: P0AD64*PLUS, beta-lactamase
#2: Chemical ChemComp-TSL / TRANS-ENAMINE INTERMEDIATE OF SULBACTAM


Mass: 235.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO5S
#3: Chemical ChemComp-MA4 / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE


Mass: 508.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H44O11
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.87 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Sep 4, 2004
RadiationMonochromator: FOCUSED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.34→30 Å / Num. all: 52442 / Num. obs: 52285 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 10.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→27.68 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1265615.9 / Data cutoff high rms absF: 1265615.9 / 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
Rfree0.194 5273 10.1 %RANDOM
Rwork0.175 ---
obs0.175 52229 99.5 %-
all-52442 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.0505 Å2 / ksol: 0.459515 e/Å3
Displacement parametersBiso mean: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2---1.5 Å20 Å2
3---0.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.34→27.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 66 264 2368
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it1.683
X-RAY DIFFRACTIONc_mcangle_it2.175
X-RAY DIFFRACTIONc_scbond_it3.684
X-RAY DIFFRACTIONc_scangle_it4.826
LS refinement shellResolution: 1.34→1.42 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 850 9.9 %
Rwork0.262 7750 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3new_cymal.parion.top
X-RAY DIFFRACTION4prodr_sul1.parnew_ligands_sul1.top
X-RAY DIFFRACTION5hepes.par

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