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- PDB-4kg6: Crystal Structure of AmpC beta-lactamase N152G Mutant from E. coli -

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Basic information

Entry
Database: PDB / ID: 4kg6
TitleCrystal Structure of AmpC beta-lactamase N152G Mutant from E. coli
ComponentsBeta-lactamase
KeywordsHYDROLASE / cephalosporinase / beta-lactamase / serine hydrolase
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: 1.75 Å
AuthorsDocter, B.E. / Baggett, V.L. / Powers, R.A. / Wallar, B.J.
CitationJournal: To be Published
Title: Complexed structures of AmpC beta-lactamase
Authors: Docter, B.E. / Baggett, V.L. / Powers, R.A. / Wallar, B.J.
History
DepositionApr 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)158,78811
Polymers158,1234
Non-polymers6657
Water27,6171533
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7213
Polymers39,5311
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7213
Polymers39,5311
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8164
Polymers39,5311
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)39,5311
Polymers39,5311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.773, 79.660, 129.288
Angle α, β, γ (deg.)90.00, 104.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Beta-lactamase / Cephalosporinase


Mass: 39530.871 Da / Num. of mol.: 4 / Mutation: N152G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ampC, ampA, b4150, JW4111 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / References: UniProt: P00811, beta-lactamase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1533 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7M potassium phosphate, 3.5mg/ml AmpC, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1.1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 162537
Reflection shellResolution: 1.75→1.81 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→27.5 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.316 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 8145 5 %RANDOM
Rwork0.15936 ---
obs0.16147 154388 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.355 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å2-1.93 Å2
2--1.95 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11114 0 35 1533 12682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211779
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211035
X-RAY DIFFRACTIONr_angle_refined_deg2.0761.94916170
X-RAY DIFFRACTIONr_angle_other_deg0.955325406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8651497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79524.758496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.515151819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2191546
X-RAY DIFFRACTIONr_chiral_restr0.130.21749
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02113663
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022715
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 593 -
Rwork0.217 11231 -
obs--98.88 %

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