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- PDB-5joc: Crystal structure of the S61A mutant of AmpC BER -

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Basic information

Entry
Database: PDB / ID: 5joc
TitleCrystal structure of the S61A mutant of AmpC BER
ComponentsBeta-lactamase
KeywordsHYDROLASE / AmpC Ber / class C beta-lactamase / S61A mutation
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / outer membrane-bounded periplasmic space / response to antibiotic / periplasmic space
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 ...: / : / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNa, J.H. / An, Y.J. / Cha, S.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structural basis for the extended substrate spectrum of AmpC BER and structure-guided discovery of the inhibition activity of citrate against the class C beta-lactamases AmpC BER and CMY-10.
Authors: Na, J.H. / Cha, S.S.
History
DepositionMay 2, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)81,8496
Polymers81,0802
Non-polymers7684
Water4,846269
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9243
Polymers40,5401
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9243
Polymers40,5401
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)207.208, 207.208, 45.635
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Beta-lactamase


Mass: 40540.031 Da / Num. of mol.: 2 / Mutation: S61A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ampC / Production host: Escherichia coli (E. coli)
References: UniProt: A7TUE6, UniProt: P00811*PLUS, beta-lactamase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 3.49 Å3/Da / Density % sol: 64.74 %
Crystal growTemperature: 295 K / Method: microbatch / Details: 25% PEG 3350, 0.1 M Citric Acid, NaOH pH 3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 109761 / % possible obs: 96.5 % / Redundancy: 5.3 % / Net I/σ(I): 29.8
Reflection shellResolution: 1.75→1.78 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data processing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F1G

1f1g


Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.156 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20015 5514 5 %RANDOM
Rwork0.17679 ---
obs0.17799 104247 96.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.604 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.23 Å20 Å2
2--0.45 Å20 Å2
3----1.46 Å2
Refinement stepCycle: 1 / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5469 0 52 269 5790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.025679
X-RAY DIFFRACTIONr_bond_other_d0.0010.025343
X-RAY DIFFRACTIONr_angle_refined_deg2.1181.9487757
X-RAY DIFFRACTIONr_angle_other_deg0.984312287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8395695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81324.463242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68515874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6411524
X-RAY DIFFRACTIONr_chiral_restr0.1450.2833
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216451
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021309
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_it2.572.4272792
X-RAY DIFFRACTIONr_mcbond_other2.5712.4272791
X-RAY DIFFRACTIONr_mcangle_it3.4183.6173483
X-RAY DIFFRACTIONr_mcangle_other3.4173.6183484
X-RAY DIFFRACTIONr_scbond_it4.1372.9422887
X-RAY DIFFRACTIONr_scbond_other4.1162.942885
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1954.2224274
X-RAY DIFFRACTIONr_long_range_B_refined7.33120.8666709
X-RAY DIFFRACTIONr_long_range_B_other7.34420.7596620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 379 -
Rwork0.259 7244 -
obs--91.58 %

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