[English] 日本語
Yorodumi- PDB-5a0z: STRUCTURE OF CUTC CHOLINE LYASE CHOLINE FREE FORM FROM KLEBSIELLA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a0z | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF CUTC CHOLINE LYASE CHOLINE FREE FORM FROM KLEBSIELLA PNEUMONIAE | ||||||
Components | CHOLINE TRIMETHYLAMINE LYASE | ||||||
Keywords | LYASE / CUTC / CHOLINE TMA LYASE / GLYCYL RADICAL ENZYME | ||||||
Function / homology | Function and homology information choline trimethylamine-lyase / carbon-nitrogen lyase activity / choline catabolic process Similarity search - Function | ||||||
Biological species | KLEBSIELLA PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Kalnins, G. / Tars, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structure and Function of Cutc Choline Lyase from Human Microbiota Bacterium Klebsiella Pneumoniaee Authors: Kalnins, G. / Kuka, J. / Grinberga, S. / Makrecka-Kuka, M. / Liepinsh, E. / Dambrova, M. / Tars, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5a0z.cif.gz | 562.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5a0z.ent.gz | 463.6 KB | Display | PDB format |
PDBx/mmJSON format | 5a0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a0z_validation.pdf.gz | 472.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5a0z_full_validation.pdf.gz | 562.8 KB | Display | |
Data in XML | 5a0z_validation.xml.gz | 105.3 KB | Display | |
Data in CIF | 5a0z_validation.cif.gz | 141.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/5a0z ftp://data.pdbj.org/pub/pdb/validation_reports/a0/5a0z | HTTPS FTP |
-Related structure data
Related structure data | 5a0uSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 89179.586 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Description: THE MICROBIAL STRAIN COLLECTION OF LATVIA / Plasmid: PRSF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL45*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.39 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 Details: 20% PEG 3350, 100-160 MM K/NA TARTRATE, 100 MM BIS-TRIS, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.984 |
Detector | Type: RAYONIX BONDED TO FIBER-OPTIC TAPERS / Detector: CCD / Date: Feb 9, 2015 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 3→61.78 Å / Num. obs: 66881 / % possible obs: 89.3 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.9 / % possible all: 76.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A0U Resolution: 3→119.92 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.771 / Cross valid method: THROUGHOUT / ESU R Free: 0.549 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 937A-946A, 980A-984A, 1004A-1017A, 1027A-1039A, 909B- 916B, 939B-946B, 981B-984B, 1006B-1015B, 1026B-1041B, , 905C- 913C, 938C- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 937A-946A, 980A-984A, 1004A-1017A, 1027A-1039A, 909B- 916B, 939B-946B, 981B-984B, 1006B-1015B, 1026B-1041B, , 905C- 913C, 938C-944C, 980C-986C, 1007C-1016C, 1029C- -1041C, 902D- 946D, 983D-985D, 997D-1017D, 1029D-1041D ARE EXCLUDED DUE TO INSUFFICIENT ELECTRON DENSITY, SIDE CHAINS OF RESIDUES 662D, 675D, 769C, 773C, 771D, 799D, 803C, 804D, 808D, 821D, 822A, 822B, 822D, 892D, 897A, 898A, 900B, 901C, 918C, 923C, 934C, 935C, 948A, 950A, 952B, 952 D, 953B, 955A, 1000B, 1000C, 1025A, 1054B, 1054C, 1076D, 1079B,1083B, 1088D, 1089A, 1089D, 1093B, 1100D, 1113D, 1114D, 1118D, 1122D, 1122B ARE MUTATED TO ALANINE DUE TO INSUFFICIENT ELECTRON DENSITY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.544 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→119.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|