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- PDB-3sh9: Crystal structure of fluorophore-labeled beta-lactamase PenP in c... -

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Basic information

Entry
Database: PDB / ID: 3sh9
TitleCrystal structure of fluorophore-labeled beta-lactamase PenP in complex with cefotaxime
ComponentsBeta-lactamase
KeywordsHYDROLASE/ANTIBIOTIC / PenP / beta-lactamase / cefotaxime / fluorophore / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Beta-lactamase / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-[6-(dimethylamino)naphthalen-2-yl]ethanone / CEFOTAXIME, C3' cleaved, open, bound form / Beta-lactamase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWong, W.-T. / Zhao, Y.-X. / Leung, Y.-C.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Increased structural flexibility at the active site of a fluorophore-conjugated beta-lactamase distinctively impacts its binding toward diverse cephalosporin antibiotics
Authors: Wong, W.-T. / Chan, K.-C. / So, P.-K. / Yap, H.-K. / Chung, W.-H. / Leung, Y.-C. / Wong, K.-Y. / Zhao, Y.-X.
History
DepositionJun 16, 2011Deposition site: RCSB / Processing site: PDBJ
SupersessionJul 27, 2011ID: 3KGN
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Non-polymer description
Revision 1.2Jun 19, 2013Group: Database references
Revision 2.0Sep 19, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Nov 1, 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_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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5176
Polymers59,2952
Non-polymers1,2214
Water4,522251
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2583
Polymers29,6481
Non-polymers6112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2583
Polymers29,6481
Non-polymers6112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.386, 91.626, 66.008
Angle α, β, γ (deg.)90.00, 104.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase / Penicillinase


Mass: 29647.660 Da / Num. of mol.: 2 / Fragment: Small exopenicillinase / Mutation: E166C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: penP / Production host: Escherichia coli (E. coli) / References: UniProt: P00808, beta-lactamase
#2: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N5O5S2
#3: Chemical ChemComp-BB0 / 1-[6-(dimethylamino)naphthalen-2-yl]ethanone


Mass: 213.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSOME RESIDUE NUMBERS ARE SIMPLY SKIPPED.

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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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF
DetectorDate: Jul 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→45.8 Å / Num. obs: 39490

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BLM

4blm


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 3.563 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24634 1983 5 %RANDOM
Rwork0.19747 ---
obs0.2 37382 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.694 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.03 Å2
2--0 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 84 251 4318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224124
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6152.0025572
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16824.919185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15315736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5591530
X-RAY DIFFRACTIONr_chiral_restr0.1240.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023066
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.22032
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22833
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.2125
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.269
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8921.52619
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49724077
X-RAY DIFFRACTIONr_scbond_it2.07431825
X-RAY DIFFRACTIONr_scangle_it3.3774.51495
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 147 -
Rwork0.213 2774 -
obs--99.97 %

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