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- PDB-3znb: METALLO-BETA-LACTAMASE (ZN, HG-BOUND FORM) -

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Basic information

Entry
Database: PDB / ID: 3znb
TitleMETALLO-BETA-LACTAMASE (ZN, HG-BOUND FORM)
ComponentsMETALLO-BETA-LACTAMASE
KeywordsHYDROLASE / BETA-LACTAMASE / METALLO BETA-LACTAMASE / MERCURY / ZINC
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 / 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 / DIFFERENCE FOURIER / Resolution: 2.7 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 15, 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 1.3Aug 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.ptnr1_label_seq_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 1.4May 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)51,1198
Polymers50,5412
Non-polymers5786
Water1,17165
1
A: METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5594
Polymers25,2701
Non-polymers2893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5594
Polymers25,2701
Non-polymers2893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.200, 78.200, 140.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: ONE ZINC AND ONE MERCURY ARE BOUND IN THE ACTIVE SITE
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: QMCN3 / 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.04 Å3/Da / Density % sol: 40 %
Crystal growpH: 7
Details: 27-29% POLYETHYLENE GLYCOL 2000, 0.1M HEPES, PH 7.0, 10UM ZNCL2, 0.3M NACL, AT ROOM TEMPERATURE. THE CRYSTALS WERE SOAKED OVERNIGHT AT ROOM TEMPERATURE IN 10MM K2HGI4 + 20MM KI.
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 mM1dropZnCl2
426-28 %PEG20001drop
526-28 %PEG20001reservoir
60.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 22, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→39 Å / Num. obs: 11371 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.045 / Net I/σ(I): 23
Reflection shellResolution: 2.7→2.87 Å / Mean I/σ(I) obs: 6.4 / Rsym value: 0.145 / % possible all: 47
Reflection
*PLUS
Rmerge(I) obs: 0.045

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1ZNB WITHOUT METALS OR SOLVENT

1znb


Resolution: 2.7→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.268 -10 %
Rwork0.2 --
obs0.2 10639 90 %
Displacement parametersBiso mean: 18.4 Å2
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 6 65 3488
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_deg2.2
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_d1.8
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: 2.7→2.83 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.311 -9.6 %
Rwork0.27 688 -
obs--47.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PARTOPCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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