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- PDB-1znb: METALLO-BETA-LACTAMASE -

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Basic information

Entry
Database: PDB / ID: 1znb
TitleMETALLO-BETA-LACTAMASE
ComponentsMETALLO-BETA-LACTAMASE
KeywordsHYDROLASE (BETA-LACTAMASE) / METALLO BETA-LACTAMASE 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / 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 / MULTIWAVELENGTH ANOMALOUS DIFFRACTION (MAD): / Resolution: 1.85 Å
AuthorsConcha, N.O. / Herzberg, O.
Citation
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.
#1: Journal: Antimicrob.Agents Chemother. / Year: 1992
Title: Biochemical Characterization of the Metallo-Beta-Lactamase Ccra from Bacteroides Fragilis
Authors: Yang, Y. / Rasmussen, B.A. / Bush, K.
History
DepositionJun 6, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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

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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)50,8498
Polymers50,5412
Non-polymers3086
Water9,494527
1
A: METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4244
Polymers25,2701
Non-polymers1543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4244
Polymers25,2701
Non-polymers1543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.298, 78.298, 140.916
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-497-

HOH

21B-498-

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
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: TAL3636 / Gene: CCRA3 / Variant: CLINICAL ISOLATE QMCN3 / Plasmid: LAMBDA DE3 / Species (production host): Escherichia coli / Gene (production host): CCRA3 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P25910, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#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.: 527 / 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: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
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

Diffraction
IDMean temperature (K)Crystal-ID
12981
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU11.5418
SYNCHROTRONNSLS X12C21.283
Detector
TypeIDDetectorDate
SIEMENS1AREA DETECTORMay 2, 1995
MARRESEARCH2IMAGE PLATEJun 12, 1995
Radiation
IDMonochromatorMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITE(002)Mx-ray1
2Mx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.2831
ReflectionResolution: 1.815→28 Å / Num. obs: 37905 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rsym value: 0.077 / Net I/σ(I): 6.7
Reflection shellResolution: 1.85→1.97 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.398 / % possible all: 95.8
Reflection
*PLUS
Num. all: 38209 / Num. measured all: 292398 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
Num. possible: 6257 / Num. unique obs: 5995 / Num. measured obs: 27319 / Rmerge(I) obs: 0.398

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MULTIWAVELENGTH ANOMALOUS DIFFRACTION (MAD):
Resolution: 1.85→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.241 -10 %
Rwork0.167 --
obs0.167 34597 91.9 %
Refine analyzeLuzzati coordinate error obs: 0.15 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3540 0 4 529 4073
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7
LS refinement shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.92 Å

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