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- PDB-9g5m: N-Acyl-D-amino-acid deacylase (D-acylase) from Klebsiella pneumon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9g5m | ||||||
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Title | N-Acyl-D-amino-acid deacylase (D-acylase) from Klebsiella pneumoniae in an open conformation | ||||||
![]() | Amidohydrolase family protein | ||||||
![]() | HYDROLASE / N-Acyl-D-amino-acid deacylase / D-acylase / amidohydrolase | ||||||
Function / homology | ![]() N-acyl-D-amino-acid deacylase / N-acyl-D-amino-acid deacylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gavira, J.A. / Martinez-Rodriguez, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Revisiting D-Acylases for D-Amino Acid Production. Authors: Martinez-Rodriguez, S. / Gavira, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.9 KB | Display | ![]() |
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PDB format | ![]() | 173.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 9gv8C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53568.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: dan, B5L96_17380, B6I68_16395, BANRA_04485, BL124_00028775, DW281_07100, EAO17_17410, FXN67_23300, G4V31_23420, GJJ08_023370, GJJ13_021835, GJJ18_03715, GNF00_21165, NCTC11679_04932, NCTC13443_ ...Gene: dan, B5L96_17380, B6I68_16395, BANRA_04485, BL124_00028775, DW281_07100, EAO17_17410, FXN67_23300, G4V31_23420, GJJ08_023370, GJJ13_021835, GJJ18_03715, GNF00_21165, NCTC11679_04932, NCTC13443_01470, NCTC5052_02702, NCTC9601_05682, NCTC9661_05441, QIG75_04865, SAMEA3499874_02915, SAMEA3499901_00964, SAMEA3512100_03687, SAMEA3515122_03158, SAMEA3538658_01149, SAMEA3538828_01003, SAMEA3673026_03520, SAMEA3720909_04521, SAMEA4364603_03367, SAMEA4873597_03320, SAMEA4873632_03948, VKR_04363 Plasmid: pET22b+ / Production host: ![]() ![]() References: UniProt: W9BIW9, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, N-acyl-D-amino-acid deacylase |
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-Non-polymers , 7 types, 397 molecules 












#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→125.72 Å / Num. obs: 34890 / % possible obs: 99.9 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.214 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.27→2.33 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.246 / Num. unique obs: 820 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→71.69 Å
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LS refinement shell | Resolution: 2.27→2.33 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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