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- PDB-1n9b: Ultrahigh resolution structure of a class A beta-lactamase: On th... -

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Basic information

Entry
Database: PDB / ID: 1n9b
TitleUltrahigh resolution structure of a class A beta-lactamase: On the mechanism and specificity of the extended-spectrum SHV-2 enzyme
ComponentsBETA-LACTAMASE SHV-2
KeywordsHYDROLASE / BETA-LACTAM HYDROLASE / PENICILLINASE / DETERGENT BINDING / DRUG DESIGN / RADIATION DAMAGE
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 / Beta-lactamase SHV-3
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsNukaga, M. / Mayama, K. / Hujer, A.M. / Bonomo, R.A. / Knox, J.R.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Ultrahigh resolution structure of a class A beta-lactamase: On the mechanism and specificity of the extended-spectrum SHV-2 enzyme
Authors: Nukaga, M. / Mayama, K. / Hujer, A.M. / Bonomo, R.A. / Knox, J.R.
History
DepositionNov 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
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 1.5Nov 6, 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-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3115
Polymers28,9371
Non-polymers1,3744
Water6,612367
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.74, 55.58, 83.30
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-2 / PENICILLINASE


Mass: 28937.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / 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: P30896, 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-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
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 1.99 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 6000, HEPES, CYMAL-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 38 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 mg/mlprotein1drop
20.56 mMCymal-6 detergent1drop
315 %(w/v)PEG60001drop
450 mMHEPES1droppH7.0
530 %PEG1reservoir
6100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.948 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 24, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 0.9→50 Å / Num. all: 164255 / Num. obs: 164255 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.4
Reflection shellResolution: 0.9→0.95 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 18796 / Rsym value: 0.5 / % possible all: 74.2
Reflection
*PLUS
Highest resolution: 0.9 Å / Lowest resolution: 50 Å / Num. obs: 161543 / % possible obs: 97 % / Num. measured all: 827345 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Highest resolution: 0.91 Å / Lowest resolution: 0.96 Å / % possible obs: 84.7 % / Num. unique obs: 20721 / Num. measured obs: 55094 / Rmerge(I) obs: 0.526

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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: 0.9→10 Å / Num. parameters: 24004 / Num. restraintsaints: 237532 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Hydrogen atoms included in refinement but not deposited; Anisotropic refinement. Coordinate error estimated from a full-matrix LS cycle is 0.020 angstroms.
RfactorNum. reflection% reflectionSelection details
Rfree0.15 8189 -RANDOM
Rwork0.125 ---
all0.1253 163646 --
obs0.125 163646 95.8 %-
Displacement parametersBiso mean: 14.5 Å2
Refine analyzeNum. disordered residues: 88 / Occupancy sum hydrogen: 2020.18 / Occupancy sum non hydrogen: 2391.85
Refinement stepCycle: LAST / Resolution: 0.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 75 375 2654
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.036
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.05
X-RAY DIFFRACTIONs_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.115
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.049
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.041
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 155457 / % reflection Rfree: 5 % / Rfactor Rfree: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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