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- PDB-4znb: METALLO-BETA-LACTAMASE (C181S MUTANT) -

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Basic information

Entry
Database: PDB / ID: 4znb
TitleMETALLO-BETA-LACTAMASE (C181S MUTANT)
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 / Resolution: 2.65 Å
AuthorsLi, Z. / Herzberg, O.
Citation
Journal: Protein Sci. / Year: 1999
Title: Structural consequences of the active site substitution Cys181 --> Ser in metallo-beta-lactamase from Bacteroides fragilis.
Authors: Li, Z. / Rasmussen, B.A. / Herzberg, O.
#1: 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.
#2: 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.
History
DepositionOct 20, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.4Mar 6, 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_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_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_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

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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)50,6866
Polymers50,5092
Non-polymers1774
Water1,838102
1
A: METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3433
Polymers25,2541
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3433
Polymers25,2541
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.000, 78.000, 139.800
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: 25254.430 Da / Num. of mol.: 2 / Mutation: C181S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: CCRA3 (WITHOUT SIGNAL SEQUENCE / Variant: CLINICAL ISOLATE QMCN3
Plasmid details: MK16 DERIVATIVE HARBORING THE T7 EXPRESSION REGION OF PET3 CLONED WITHIN THE TETRACYCLINE RESISTANCE MARKER
Plasmid: PCLL2216 / Species (production host): Escherichia coli / Gene (production host): CCRA3 (WITHOUT SIGNAL SEQUENCE) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (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-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.: 102 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYS 181 IS REPLACED BY SER. THE ZN2 SITE IS UNOCCUPIED.

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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: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
210 mMHEPES1drop
30.01 mM1dropZnCl2
40.3 M1dropNaCl
526-28 %PEG20001reservoir
60.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→10.9 Å / Num. obs: 12469 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.143 / Rsym value: 0.143 / Net I/σ(I): 2
Reflection shellResolution: 2.65→2.82 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2 / Rsym value: 0.452 / % possible all: 83
Reflection shell
*PLUS
% possible obs: 83 % / Num. unique obs: 1781

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.65→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT (ALMOST) / σ(F): 2 / Details: OVERALL R IS 0.177 (WORK+TEST SET)
RfactorNum. reflection% reflectionSelection details
Rfree0.25 831 8 %RANDOM
Rwork0.173 ---
obs0.173 10349 95 %-
Refinement stepCycle: LAST / Resolution: 2.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 4 102 3499
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.6
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_d
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19_CA.IONTOPH19_CA.ION
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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