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- PDB-4kg5: Crystal Structure of AmpC beta-lactamase N152G Mutant in Complex ... -

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Basic information

Entry
Database: PDB / ID: 4kg5
TitleCrystal Structure of AmpC beta-lactamase N152G Mutant in Complex with Cefotaxime
ComponentsBeta-lactamase
KeywordsHydrolase/antibiotic / Cephalosporinase / beta-lactamase / serine hydrolase / acyl-enzyme complex / Hydrolase-antibiotic complex
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
CEFOTAXIME, C3' cleaved, open, bound form / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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 2.0Sep 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
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 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)160,18813
Polymers158,1234
Non-polymers2,0659
Water8,935496
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2135
Polymers39,5311
Non-polymers6824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0233
Polymers39,5311
Non-polymers4922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9282
Polymers39,5311
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0233
Polymers39,5311
Non-polymers4922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.367, 80.348, 129.790
Angle α, β, γ (deg.)90.00, 103.99, 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.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.94 %
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-D / Wavelength: 1.1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 91517
Reflection shellResolution: 2.11→2.18 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→28.23 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.155 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23179 4580 5 %RANDOM
Rwork0.17899 ---
obs0.18171 86783 96.81 %-
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: 36.593 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å2-0.73 Å2
2--1.96 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.11→28.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11020 0 129 496 11645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211597
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210742
X-RAY DIFFRACTIONr_angle_refined_deg1.921.95515913
X-RAY DIFFRACTIONr_angle_other_deg0.893324643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9851451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98924.702487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.024151711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3611545
X-RAY DIFFRACTIONr_chiral_restr0.1080.21724
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113437
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022696
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: 2.11→2.162 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 307 -
Rwork0.247 5906 -
obs--89.56 %

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