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- PDB-1shv: STRUCTURE OF SHV-1 BETA-LACTAMASE -

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Basic information

Entry
Database: PDB / ID: 1shv
TitleSTRUCTURE OF SHV-1 BETA-LACTAMASE
ComponentsPROTEIN (BETA-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 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-1 / Beta-lactamase SHV-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsKuzin, A.P. / Nukaga, M. / Nukaga, Y. / Hujer, A. / Bonomo, R.A. / Knox, J.R.
CitationJournal: Biochemistry / Year: 1999
Title: Structure of the SHV-1 beta-lactamase.
Authors: Kuzin, A.P. / Nukaga, M. / Nukaga, Y. / Hujer, A.M. / Bonomo, R.A. / Knox, J.R.
History
DepositionFeb 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (BETA-LACTAMASE SHV-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4162
Polymers28,9071
Non-polymers5091
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.600, 55.600, 87.000
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 PROTEIN (BETA-LACTAMASE SHV-1) / BETA-LACTAMASE PIT-2 / PENICILLINASE


Mass: 28907.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 1 DETERGENT MOLECULE (CYMAL-6) BOUND NON-COVALENTLY
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.: 1 / Source method: obtained synthetically / Formula: C24H44O11
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsDETERGENT USED IN CRYSTALLIZATION
Sequence detailsWE USE A CONSENSUS NUMBERING IN WHICH 239 AND 253 ARE NOT USED FOR THIS ENZYME. HERE, 238 AND 240 ...WE USE A CONSENSUS NUMBERING IN WHICH 239 AND 253 ARE NOT USED FOR THIS ENZYME. HERE, 238 AND 240 ARE LINKED, AS ARE 252 AND 254. TER ARG: NUMBERING FOR THE MATURE PROTEIN STARTS AT 26 (USING A CONSENSUS CONVENTION).

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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 growpH: 7
Details: VAPOR DIFFUSION, WITH 2MG/ML PROTEIN IN 15% PEG6000, 50MM HEPES PH7.0 0.65MM CYMAL-6, OVER 30% PEG RESERVOIR AT ROOM TEMPERATURE
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mg/mlprotein1drop
20.56 mMCymal-61drop
315 %PEG60001drop
450 mMHEPES1drop
530 %PEG1reservoir
6100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1998 / Details: 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: 1.96→43 Å / Num. obs: 49725 / % possible obs: 0.85 % / Redundancy: 3.3 % / Rsym value: 0.065 / Net I/σ(I): 15.5
Reflection shellResolution: 1.96→2.09 Å / Redundancy: 1.95 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.194 / % possible all: 0.4
Reflection
*PLUS
Num. obs: 15082 / % possible obs: 85 % / Num. measured all: 49725 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 40 % / Num. unique obs: 1156 / Num. measured obs: 2259 / Rmerge(I) obs: 0.194

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XPB

1xpb


Resolution: 1.98→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: NO IDEAL GEOMETRY FOR DETERGENT MOLECULE.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 978 6.7 %RANDOM
Rwork0.182 ---
obs-13653 84.4 %-
Displacement parametersBiso mean: 14.7 Å2
Refine analyzeLuzzati coordinate error free: 0.205 Å
Refinement stepCycle: LAST / Resolution: 1.98→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 35 81 2140
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.75
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.49
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.98→2.06 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.255 42 6.7 %
Rwork0.255 752 -
obs--35.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARALLHDG.PROTOPALLHDG.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARM.MA1TOPH.MA1
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.49

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