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- PDB-3m2j: Crystal Structure of fluorescein-labeled Class A -lactamase PenP -

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Basic information

Entry
Database: PDB / ID: 3m2j
TitleCrystal Structure of fluorescein-labeled Class A -lactamase PenP
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / fluorophore / biosensor / Antibiotic resistance / Cell membrane / Lipoprotein / Membrane / Palmitate
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
Chem-F5M / Beta-lactamase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhao, Y.X. / Leung, Y.C. / Wong, W.T.
CitationJournal: To be Published
Title: Crystal Structure of fluorescein-labeled Class A -lactamase PenP
Authors: Zhao, Y.X. / Leung, Y.C. / Wong, W.T.
History
DepositionMar 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _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: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8085
Polymers57,1892
Non-polymers6193
Water4,576254
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1183
Polymers28,5941
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6902
Polymers28,5941
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.354, 92.340, 66.415
Angle α, β, γ (deg.)90.00, 104.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase / Penicillinase / Large exopenicillinase / Small exopenicillinase


Mass: 28594.348 Da / Num. of mol.: 2 / Fragment: residues 47-301 / Mutation: E166C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: 749/C / Gene: penP / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00808, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-F5M / 5-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)-2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid / fluorescein-5-maleimide


Mass: 427.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H13NO7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF
DetectorDate: Nov 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→46 Å / Num. obs: 45125 / Rmerge(I) obs: 0.084

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Processing

Software
NameVersionClassification
CrystalCleardata collection
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BLM

4blm


Resolution: 1.8→31.59 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.897 / SU B: 4.195 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27278 2274 5.1 %RANDOM
Rwork0.20901 ---
obs0.21221 42614 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4007 0 42 254 4303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224103
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.221.9925549
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4055503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04224.946186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.75715740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6361530
X-RAY DIFFRACTIONr_chiral_restr0.1920.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023044
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2720.22066
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22794
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0771.52642
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73124103
X-RAY DIFFRACTIONr_scbond_it2.76131694
X-RAY DIFFRACTIONr_scangle_it4.1114.51446
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 102 -
Rwork0.322 2160 -
obs--66.45 %

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