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- PDB-2gkl: Crystal structure of the zinc carbapenemase CPHA in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2gkl
TitleCrystal structure of the zinc carbapenemase CPHA in complex with the inhibitor pyridine-2,4-dicarboxylate
ComponentsBeta-lactamase
KeywordsHYDROLASE / LACTAMASE / INHIBITOR / ZN
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDINE-2,4-DICARBOXYLIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsGarau, G. / Dideberg, O.
Citation
Journal: Antimicrob.Agents Chemother. / Year: 2007
Title: Competitive Inhibitors of the CphA Metallo-{beta}-Lactamase from Aeromonas hydrophila
Authors: Horsfall, L.E. / Garau, G. / Lienard, B.M.R. / Dideberg, O. / Schofield, C.J. / Frere, J.M. / Galleni, M.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: A metallo-beta-lactamase enzyme in action: crystal structures of the monozinc carbapenemase CphA and its complex with biapenem
Authors: Garau, G. / Bebrone, C. / Anne, C. / Galleni, M. / Frere, J.M. / Dideberg, O.
#2: Journal: Antimicrob.Agents Chemother. / Year: 2004
Title: Update of the standard numbering scheme for class B beta-lactamases
Authors: Garau, G. / Garcia-Saez, I. / Bebrone, C. / Anne, C. / Mercuri, P. / Galleni, M. / Frere, J.M. / Dideberg, O.
#3: Journal: Embo J. / Year: 1995
Title: The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold
Authors: Carfi, A. / Pares, S. / Duee, E. / Galleni, M. / Duez, C. / Frere, J.M. / Dideberg, O.
History
DepositionApr 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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.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: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7306
Polymers25,2211
Non-polymers5095
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.638, 101.211, 117.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

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Components

#1: Protein Beta-lactamase /


Mass: 25220.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: cphA / Plasmid: PUC20-CPHA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P26918, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PD2 / PYRIDINE-2,4-DICARBOXYLIC ACID / Lutidinic acid


Mass: 167.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS COORDINATES USE NON-SEQUENTIAL RESIDUE NUMBERING. THE NUMBERING RELATES TO PDB ENTRY 1X8H.

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG, AS, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 21756 / Num. obs: 21647 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 7.4
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 6 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.179 / % possible all: 97.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
REFMAC5.2.0019refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X8H

1x8h


Resolution: 1.86→21.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.188 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.12 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19617 1102 5.1 %RANDOM
Rwork0.15898 ---
all0.161 21625 --
obs0.16084 20495 99.29 %-
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: 14.148 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.86→21.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 31 190 1979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221835
X-RAY DIFFRACTIONr_bond_other_d0.0070.021239
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9742476
X-RAY DIFFRACTIONr_angle_other_deg1.2183.0013021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92223.92479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.365159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02359
X-RAY DIFFRACTIONr_nbd_refined0.3590.2439
X-RAY DIFFRACTIONr_nbd_other0.2050.21340
X-RAY DIFFRACTIONr_nbtor_refined0.180.2888
X-RAY DIFFRACTIONr_nbtor_other0.0880.2863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2169
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.228
X-RAY DIFFRACTIONr_mcbond_it0.7581.51130
X-RAY DIFFRACTIONr_mcbond_other0.2051.5451
X-RAY DIFFRACTIONr_mcangle_it1.18121784
X-RAY DIFFRACTIONr_scbond_it2.1853800
X-RAY DIFFRACTIONr_scangle_it3.4744.5692
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 77 -
Rwork0.162 1425 -
obs--95.24 %

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