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- PDB-4qd4: Structure of ADC-68, a Novel Carbapenem-Hydrolyzing Class C Exten... -

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Basic information

Entry
Database: PDB / ID: 4qd4
TitleStructure of ADC-68, a Novel Carbapenem-Hydrolyzing Class C Extended-Spectrum -Lactamase from Acinetobacter baumannii
ComponentsBeta-lactamase ADC-68
KeywordsHYDROLASE / Beta-lactamase / HYDROLASE-HYDROLASE INHIBITOR 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
CITRIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHong, M.K. / Kang, L.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of ADC-68, a novel carbapenem-hydrolyzing class C extended-spectrum beta-lactamase isolated from Acinetobacter baumannii
Authors: Jeon, J.H. / Hong, M.K. / Lee, J.H. / Lee, J.J. / Park, K.S. / Karim, A.M. / Jo, J.Y. / Kim, J.H. / Ko, K.S. / Kang, L.W. / Lee, S.H.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase ADC-68
B: Beta-lactamase ADC-68
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1606
Polymers81,3852
Non-polymers7754
Water7,746430
1
A: Beta-lactamase ADC-68
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0803
Polymers40,6921
Non-polymers3872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase ADC-68
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0803
Polymers40,6921
Non-polymers3872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.393, 71.006, 179.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase ADC-68


Mass: 40692.426 Da / Num. of mol.: 2 / Fragment: UNP residues 24-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaADC-68 / Production host: Escherichia coli (E. coli) / References: UniProt: R4NH29
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M carboxylic acids, 0.1M buffer system 1 pH 6.5, 30% P550MME_P20K, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 65468 / % possible obs: 96.2 % / Observed criterion σ(F): 4.4 / Observed criterion σ(I): 127.4
Reflection shellResolution: 1.8→1.86 Å / % possible all: 90.7

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→35.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.209 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23559 3319 5.1 %RANDOM
Rwork0.18837 ---
obs0.19085 62076 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.871 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5680 0 50 430 6160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.025862
X-RAY DIFFRACTIONr_bond_other_d0.0010.025646
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.9737944
X-RAY DIFFRACTIONr_angle_other_deg0.963313050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1635712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.61225.878262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.645151034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6271512
X-RAY DIFFRACTIONr_chiral_restr0.1360.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216618
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021298
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.797→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 221 -
Rwork0.268 4170 -
obs--88.58 %

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