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- PDB-2bga: Bacillus cereus metallo-beta-lactamase (BcII) Arg (121) Cys mutan... -

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Basic information

Entry
Database: PDB / ID: 2bga
TitleBacillus cereus metallo-beta-lactamase (BcII) Arg (121) Cys mutant. Solved at pH7 using 20 Micromolar ZnSO4 in the buffer. 1mM DTT was used as a reducing agent. Cys221 is oxidized.
ComponentsBETA-LACTAMASE II
KeywordsHYDROLASE / ZINC / METALLO-BETA-LACTAMASE / ANTIBIOTIC RESISTANCE
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 / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase ...: / 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 / 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
AZIDE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDavies, A.M. / Rasia, R.M. / Vila, A.J. / Sutton, B.J. / Fabiane, S.M.
Citation
Journal: Biochemistry / Year: 2005
Title: Effect of Ph on the Active Site of an Arg121Cys Mutant of the Metallo-Beta-Lactamase from Bacillus Cereus: Implications for the Enzyme Mechanism
Authors: Davies, A.M. / Rasia, R.M. / Vila, A.J. / Sutton, B.J. / Fabiane, S.M.
#1: Journal: Biochemistry / Year: 2002
Title: Exploring the Role and Binding Affinity of a Second Zinc Equivalent in B. Cereus Metallo-Beta-Lactamase
Authors: Rasia, R.M. / Vila, A.J.
#2: Journal: Biochemistry / Year: 1998
Title: Crystal Structure of the Zinc-Dependent Beta-Lactamase from Bacillus Cereus at 1.9A Resolution: Binuclear Active Site with Features of a Mononuclear Enzyme
Authors: Fabiane, S.M. / Sohi, M.K. / Wan, T. / Payne, D.J. / Bateson, J.H. / Mitchell, T. / Sutton, B.J.
History
DepositionDec 17, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,91015
Polymers49,9472
Non-polymers96313
Water3,891216
1
A: BETA-LACTAMASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5459
Polymers24,9731
Non-polymers5728
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-LACTAMASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3656
Polymers24,9731
Non-polymers3925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.391, 67.391, 178.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2065-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.08787, 0.28805, 0.95357), (0.29389, -0.92216, 0.25148), (0.95179, 0.25815, -0.16569)
Vector: 19.92278, 16.48327, -27.82709)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BETA-LACTAMASE II / METALLO-BETA-LACTAMASE / PENICILLINASE / CEPHALOSPORINASE


Mass: 24973.480 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Strain: 569/H/9 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04190, beta-lactamase

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Non-polymers , 5 types, 229 molecules

#2: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 121 ARG ENGINEERED RESIDUE IN CHAIN B, CYS 121 ARG BETA-LACTAM + ...ENGINEERED RESIDUE IN CHAIN A, CYS 121 ARG ENGINEERED RESIDUE IN CHAIN B, CYS 121 ARG BETA-LACTAM + H2O = SUBSTITUTED BETA-AMINO ACID.
Has protein modificationY
Sequence detailsTHE SEQUENCE NUMBERING USED IN THIS ENTRY IS BASED ON A STANDARD NUMBERING SYSTEM DEVISED TO ALLOW ...THE SEQUENCE NUMBERING USED IN THIS ENTRY IS BASED ON A STANDARD NUMBERING SYSTEM DEVISED TO ALLOW FOR EASY COMPARISON BETWEEN DIFFERENT MEMBERS OF THE BACILLUS CEREUS METALLO-BETA-LACTAMASE FAMILY. SEE ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, MAR. 2001, VOL 45, P660-663

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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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PROTEIN WAS CRYSTALLISED USING HANGING DROP VAPOR DIFFUSION. RESERVOIR SOLUTION CONTAINED 100MM TRIS AT PH4.5-5, 70-75% AMMONIUM SULPHATE, 1MM DTT OR 1MM DTT AND 1MM TCEP-HCL, 2MM ZNSO4 AND ...Details: PROTEIN WAS CRYSTALLISED USING HANGING DROP VAPOR DIFFUSION. RESERVOIR SOLUTION CONTAINED 100MM TRIS AT PH4.5-5, 70-75% AMMONIUM SULPHATE, 1MM DTT OR 1MM DTT AND 1MM TCEP-HCL, 2MM ZNSO4 AND 0.1% AZIDE. PROTEIN CONCENTRATION OF 2.7 MG/ML. DROPS WERE KEPT AT 291K AND WERE STREAK SEEDED FROM A WILD TYPE CRYSTAL AFTER 1 DAY., pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 19, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.7→2.77 Å / Num. obs: 13382 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 4
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BC2

1bc2


Resolution: 2.7→6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 659 4.9 %RANDOM
Rwork0.1856 ---
obs0.1856 13382 99.1 %-
Solvent computationBsol: 39.64 Å2 / ksol: 0.376 e/Å3
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3355 0 51 216 3622
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.93
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.799
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 13

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