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- PDB-2znb: METALLO-BETA-LACTAMASE (CADMIUM-BOUND FORM) -

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Basic information

Entry
Database: PDB / ID: 2znb
TitleMETALLO-BETA-LACTAMASE (CADMIUM-BOUND FORM)
ComponentsMETALLO-BETA-LACTAMASE
KeywordsHYDROLASE / BETA-LACTAMASE / METALLO BETA-LACTAMASE / CADMIUM
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.15 Å
AuthorsConcha, N.O. / Herzberg, O.
Citation
Journal: Protein Sci. / Year: 1997
Title: Crystal structures of the cadmium- and mercury-substituted metallo-beta-lactamase from Bacteroides fragilis.
Authors: Concha, N.O. / Rasmussen, B.A. / Bush, K. / Herzberg, O.
#1: Journal: Structure / Year: 1996
Title: Crystal Structure of the Wide-Spectrum Binuclear Zinc Beta-Lactamase from Bacteroides Fragilis
Authors: Concha, N.O. / Rasmussen, B.A. / Bush, K. / Herzberg, O.
#2: Journal: Antimicrob.Agents Chemother. / Year: 1992
Title: Biochemical Characterization of the Metallo-Beta-Lactamase Ccra from Bacteroides Fragilis Tal3636
Authors: Yang, Y. / Rasmussen, B.A. / Bush, K.
History
DepositionOct 14, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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.ptnr2_auth_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METALLO-BETA-LACTAMASE
B: METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0378
Polymers50,5412
Non-polymers4966
Water5,170287
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A: METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5184
Polymers25,2701
Non-polymers2483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5184
Polymers25,2701
Non-polymers2483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.086, 78.086, 139.746
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-303-

HOH

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Components

#1: Protein METALLO-BETA-LACTAMASE / CLASS B BETA-LACTAMASE


Mass: 25270.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CADMIUM IS BOUND IN THE ACTIVE SITE BINUCLEAR CENTER
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: QMCN3 / Cell line: BL21 / Gene: CCRA3 (WITHOUT SIGNAL SEQUENCE)
Plasmid details: MK16 DERIVATIVE HARBORING THE T7 EXPRESSION REGION OF PET3 CLONED WITHIN THE TETRACYCLINE RESISTANCE MARKER
Plasmid: PCLL2216 / Gene (production host): CCRA3 (WITHOUT SIGNAL SEQUENCE) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 LAMBDA DE3 / References: UniProt: P25910, beta-lactamase
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growpH: 7
Details: 26-28%POLYETHYLENE GLYCOL 4000, 0.1M HEPES, PH 7.0, 0.3M NACL, 10UM CDCL2, AT ROOM TEMPERATURE
Temp details: room temp
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Concha, N.O., (1996) Structure (London), 4, 823.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-8 mg/mlprotein1drop
255 mMHEPES1drop
30.01 mM1dropCdCl2
426-28 %PEG20001drop
526-28 %PEG20001reservoir
60.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1
DetectorDetector: CCD / Date: May 30, 1996
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→29 Å / Num. obs: 26096 / % possible obs: 87.4 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rsym value: 0.07
Reflection shellResolution: 2.15→2.33 Å / Rsym value: 0.198 / % possible all: 74.1
Reflection
*PLUS
Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
PROCORdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1ZNB WITHOUT METALS OR SOLVENT

1znb


Resolution: 2.15→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / σ(F): 2
Details: RESIDUES PRO A 249, LYS B 248, AND PRO B 249 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.259 -10 %
Rwork0.182 --
obs0.182 21210 87.4 %
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 4 287 3678
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.15→2.25 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.326 229 8.5 %
Rwork0.26 2048 -
obs--70.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 21210 / Num. reflection obs: 20370
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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