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Open data
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Basic information
Entry | Database: PDB / ID: 2oqc | ||||||
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Title | Crystal Structure of Penicillin V acylase from Bacillus subtilis | ||||||
![]() | Penicillin V acylase | ||||||
![]() | HYDROLASE / NTN-HYDROLASE / PENICILLIN V ACYLASE / CONJUGATED BILE ACID HYDROLASE / CHOLOYLGLYCINE HYDROLASE / BACILLUS SUBTILIS | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Suresh, C.G. / Rathinaswamy, P. / Pundle, A.V. / Prabhune, A.A. / Sivaraman, H. / Brannigan, J.A. / Dodson, G.G. | ||||||
![]() | ![]() Title: Crystal Structure of Penicillin V acylase from Bacillus subtilis Authors: Suresh, C.G. / Rathinaswamy, P. / Pundle, A.V. / Prabhune, A.A. / Sivaraman, H. / Brannigan, J.A. / Dodson, G.G. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Cloning, purification, crystallization and preliminary structural studies of penicillin V acylase from Bacillus subtilis Authors: Rathinaswamy, P. / Pundle, A.V. / Prabhune, A.A. / Sivaraman, H. / Brannigan, J.A. / Dodson, G.G. / Suresh, C.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.9 KB | Display | ![]() |
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PDB format | ![]() | 115.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.1 KB | Display | ![]() |
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Full document | ![]() | 463.8 KB | Display | |
Data in XML | ![]() | 31.5 KB | Display | |
Data in CIF | ![]() | 45.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pvaS S: Starting model for refinement |
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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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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 4 / Auth seq-ID: 1 - 329 / Label seq-ID: 1 - 327
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Components
#1: Protein | Mass: 37038.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q2HPP6, UniProt: P54948*PLUS, penicillin amidase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 4M sodium formate in 100mM Tris-HCl buffer, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 7, 2002 / Details: MIRRORS |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.497→20 Å / Num. obs: 31859 / Biso Wilson estimate: 40.76 Å2 |
Reflection shell | Resolution: 2.497→2.562 Å / % possible all: 96.24 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PVA Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.252 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.756 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2541 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.497→2.562 Å / Total num. of bins used: 20
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