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- PDB-1zkj: Structural Basis for the Extended Substrate Spectrum of CMY-10, a... -

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Basic information

Entry
Database: PDB / ID: 1zkj
TitleStructural Basis for the Extended Substrate Spectrum of CMY-10, a Plasmid-Encoded Class C beta-lactamase
Componentsextended-spectrum beta-lactamaseBeta-lactamase
KeywordsHYDROLASE / extended spectrum beta-lactamase / CMY-10 / plasmid / class C
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / nucleotide binding / response to antibiotic / metal ion binding
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
ACETIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCha, S.S. / Jung, H.I. / An, Y.J. / Lee, S.H.
CitationJournal: Mol.Microbiol. / Year: 2006
Title: Structural basis for the extended substrate spectrum of CMY-10, a plasmid-encoded class C beta-lactamase.
Authors: Kim, J.Y. / Jung, H.I. / An, Y.J. / Lee, J.H. / Kim, S.J. / Jeong, S.H. / Lee, K.J. / Suh, P.G. / Lee, H.S. / Lee, S.H. / Cha, S.S.
History
DepositionMay 3, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: extended-spectrum beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,10713
Polymers38,3431
Non-polymers76312
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.703, 59.296, 63.856
Angle α, β, γ (deg.)90.00, 103.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein extended-spectrum beta-lactamase / Beta-lactamase / CMY-10


Mass: 38343.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter aerogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q99QC1, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.25 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Zinc Acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 Å
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Jul 10, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 1.55→22.11 Å / Num. obs: 267900 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 1.9 Å2
Reflection shellResolution: 1.55→1.6 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
PROTEUM PLUSdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1170233.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 2379 10.3 %RANDOM
Rwork0.2086 ---
obs0.21 23088 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.9393 Å2 / ksol: 0.438244 e/Å3
Displacement parametersBiso mean: 10.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å21.21 Å2
2---0.35 Å20 Å2
3---0.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.05 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 8 400 3035
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellHighest resolution: 1.55 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork3676 -
Rfree-9.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2acet.paramacet.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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