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- PDB-2bg8: Bacillus cereus metallo-beta-lactamase (BcII) Arg (121) Cys mutan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bg8 | ||||||
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Title | Bacillus cereus metallo-beta-lactamase (BcII) Arg (121) Cys mutant. Solved at pH4.5 using 20 Micromolar ZnSO4 in the buffer. 1mM DTT and 1mM TCEP-HCl were used as reducing agents. | ||||||
![]() | (BETA-LACTAMASE ...) x 2 | ||||||
![]() | HYDROLASE / ANTIBIOTIC RESISTANCE | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Davies, A.M. / Rasia, R.M. / Vila, A.J. / Sutton, B.J. / Fabiane, S.M. | ||||||
![]() | ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.9 KB | Display | ![]() |
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PDB format | ![]() | 82.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.6 KB | Display | ![]() |
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Full document | ![]() | 480.4 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bfkC ![]() 2bflC ![]() 2bfzC ![]() 2bg2C ![]() 2bg6C ![]() 2bg7C ![]() 2bgaC ![]() 1bc2S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.09026, 0.29149, 0.95231), Vector: |
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Components
-BETA-LACTAMASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 24957.482 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 24941.482 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 311 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 121 ARG ENGINEERED RESIDUE IN CHAIN B, CYS 121 ARG BETA-LACTAM + ...ENGINEERED |
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Sequence details | THE 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 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 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 4.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 31, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→58 Å / Num. obs: 16423 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 38.34 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.5→2.57 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BC2 Resolution: 2.5→6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Bsol: 63.45 Å2 / ksol: 0.367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8 /
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