[English] 日本語
![](img/lk-miru.gif)
- PDB-2bg7: Bacillus cereus metallo-beta-lactamase (BcII) Arg (121) Cys mutan... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2bg7 | ||||||
---|---|---|---|---|---|---|---|
Title | Bacillus cereus metallo-beta-lactamase (BcII) Arg (121) Cys mutant. Solved at pH4.5 using 20 Micromolar ZnSO4 in the buffer. 1mM DTT was used as a reducing agent. Cys221 is oxidized. | ||||||
![]() | BETA-LACTAMASE II | ||||||
![]() | 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 109.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 82.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 481.9 KB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 33.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bfkC ![]() 2bflC ![]() 2bfzC ![]() 2bg2C ![]() 2bg6C ![]() 2bg8C ![]() 2bgaC ![]() 1bc2S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
2 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.08873, 0.28519, 0.95436), Vector: |
-
Components
#1: Protein | Mass: 24957.482 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 121 ARG ENGINEERED RESIDUE IN CHAIN B, CYS 121 ARG BETA-LACTAM + ...ENGINEERED | 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: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.9 % |
---|---|
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 2.7MG/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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 30, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9755 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→59.76 Å / Num. obs: 28092 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4 / % possible all: 92.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BC2 Resolution: 2.1→6 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 70.21 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rwork: 0.2224 / Total num. of bins used: 8 |