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- PDB-3fkw: AmpC K67R mutant apo structure -

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Basic information

Entry
Database: PDB / ID: 3fkw
TitleAmpC K67R mutant apo structure
ComponentsBeta-lactamase
KeywordsHYDROLASE / AmpC / K67R / beta-lactamase / general base / Antibiotic resistance / Periplasm
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 Å
AuthorsChen, Y. / McReynolds, A. / Shoichet, B.K.
CitationJournal: Protein Sci. / Year: 2009
Title: Re-examining the role of Lys67 in class C beta-lactamase catalysis.
Authors: Chen, Y. / McReynolds, A. / Shoichet, B.K.
History
DepositionDec 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)79,5566
Polymers79,2322
Non-polymers3244
Water17,096949
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8063
Polymers39,6161
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7503
Polymers39,6161
Non-polymers1342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-30 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.348, 76.564, 97.702
Angle α, β, γ (deg.)90.000, 115.820, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / E.C.3.5.2.6 / AmpC beta-lactamase / Cephalosporinase


Mass: 39615.938 Da / Num. of mol.: 2 / Fragment: residues 20-377 / Mutation: K67R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ampA, ampC, b4150, JW4111 / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 949 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: Potassium Phosphate, pH 8.7, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2006 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.498→88.05 Å / Num. obs: 120185 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.051 / Χ2: 1.048 / Net I/σ(I): 16.662
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.498-1.552.30.513112871.11290.9
1.55-1.622.40.38116821.06593.5
1.62-1.692.40.281118301.0694.7
1.69-1.782.40.191119631.05695.3
1.78-1.892.40.134119681.07295.8
1.89-2.042.50.083121151.02196.3
2.04-2.242.50.059121371.05696.8
2.24-2.562.50.048122490.97697.4
2.56-3.232.50.036123960.98598.3
3.23-502.40.035125581.09498.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1KE4

1ke4


Resolution: 1.498→88.05 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.88 / SU B: 2.665 / SU ML: 0.046 / SU R Cruickshank DPI: 0.093 / SU Rfree: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.199 6055 5 %RANDOM
Rwork0.166 ---
obs0.167 120176 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.55 Å2 / Biso mean: 18.082 Å2 / Biso min: 7.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20.7 Å2
2---0.51 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.498→88.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5889 0 16 949 6854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226115
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9528426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7335816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70524.652273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.903151031
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5751531
X-RAY DIFFRACTIONr_chiral_restr0.0820.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024761
X-RAY DIFFRACTIONr_nbd_refined0.2020.23122
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2780
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.253
X-RAY DIFFRACTIONr_mcbond_it0.7831.53726
X-RAY DIFFRACTIONr_mcangle_it1.29926087
X-RAY DIFFRACTIONr_scbond_it2.13132419
X-RAY DIFFRACTIONr_scangle_it2.8534.52288
X-RAY DIFFRACTIONr_rigid_bond_restr1.6236145
X-RAY DIFFRACTIONr_sphericity_free3.3193951
X-RAY DIFFRACTIONr_sphericity_bonded2.26835904
LS refinement shellResolution: 1.498→1.537 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 403 -
Rwork0.241 7671 -
all-8074 -
obs--87.46 %

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