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

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Basic information

Entry
Database: PDB / ID: 2bfk
TitleBacillus cereus metallo-beta-lactamase (BcII) Arg (121) Cys mutant. Solved at pH7 using 20mM ZnSO4 in buffer. 1mM DTT was used as a reducing agent
ComponentsBETA-LACTAMASE II
KeywordsHYDROLASE / ZINC / METALLO-BETA-LACTAMASE / ANTIBIOTIC RESISTANCE
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 superfamily / 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / 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 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 the 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 7, 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 / 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
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
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 / struct_site
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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_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: BETA-LACTAMASE II
B: BETA-LACTAMASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,99027
Polymers49,8832
Non-polymers2,10725
Water9,278515
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A: BETA-LACTAMASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,13115
Polymers24,9411
Non-polymers1,19014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-LACTAMASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,85912
Polymers24,9411
Non-polymers91811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.311, 67.311, 178.010
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-2167-

HOH

21A-2206-

HOH

31B-2149-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.09333, 0.30113, 0.94901), (0.28926, -0.92025, 0.26356), (0.95269, 0.24991, -0.17299)
Vector: 19.47756, 16.56312, -27.6956)

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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: 24941.482 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, 540 molecules

#2: Chemical ChemComp-AZI / AZIDE ION


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


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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.
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: ESRF / Beamline: ID13 / Wavelength: 0.96
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 13, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2→58.72 Å / Num. obs: 37787 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 11 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.4
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.1 / % possible all: 99.9

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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→6 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 3591 5 %RANDOM
Rwork0.1721 ---
obs0.1721 71090 99.9 %-
Solvent computationBsol: 85.5 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 25.31 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 121 515 4028
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_deg1.39
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
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→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2181 215 -
Rwork0.1715 9496 -
obs--99.9 %

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