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Yorodumi- PDB-3kzs: Crystal structure of glycosyl hydrolase family 5 (NP_809925.1) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kzs | ||||||
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Title | Crystal structure of glycosyl hydrolase family 5 (NP_809925.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution | ||||||
Components | glycosyl hydrolase family 5 | ||||||
Keywords | HYDROLASE / glycosyl hydrolase family 5 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information Putative collagen-binding domain / Putative collagen-binding domain of a collagenase / Putative glycohydrolase domain DUF4038 / Protein of unknown function (DUF4038) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of glycosyl hydrolase family 5 (NP_809925.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kzs.cif.gz | 481.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kzs.ent.gz | 408.5 KB | Display | PDB format |
PDBx/mmJSON format | 3kzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kzs_validation.pdf.gz | 512 KB | Display | wwPDB validaton report |
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Full document | 3kzs_full_validation.pdf.gz | 572.8 KB | Display | |
Data in XML | 3kzs_validation.xml.gz | 85.5 KB | Display | |
Data in CIF | 3kzs_validation.cif.gz | 126.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/3kzs ftp://data.pdbj.org/pub/pdb/validation_reports/kz/3kzs | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 54546.570 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: VPI-5482 / Gene: BT_1012 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A905 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MRD / ( #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.20M ammonium sulfate, 40.0% 2-methyl-2,4-pentanediol, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162,0.97870,0.97814 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 13, 2008 / Details: Flat mirror (vertical focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→85.176 Å / Num. all: 139171 / Num. obs: 139171 / % possible obs: 100 % / Redundancy: 6.4 % / Rsym value: 0.124 / Net I/σ(I): 11.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→85.176 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 4.557 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.186 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3) AFTER BUILDING THE PROTEIN CHAINS A, B AND C, ANOMALOUS DIFFERENCE MAPS AND DIFFERENCE ELECTRON DENSITY MAPS SUGGESTED THAT THERE WAS A FOURTH SUBUNIT IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. HOWEVER, THE ELECTRON DENSITY FOR THIS SUBUNIT IS POOR, AND BOTH THE ELECTRON DENSITY MAP AND ANOMALOUS DIFFERENCE FOURIER MAPS INDICATE THAT THIS EXTRA SUBUNIT IS DISORDERED. THE ANOMALOUS DIFFERENCE PEAKS WERE USED TO GUIDE THE BUILDING OF CHAIN D. THE PATTERN OF ANOMALOUS DIFFERENCE DENSITY PEAKS SUPPORTS MODELING OF THE SUBUNIT IN TWO HALF OCCUPANCY CONFORMATIONS. NOTE THAT WHILE CHAIN D PART B WOULD SYMMETRY CLASH WITH ITSELF, IT DOES NOT CLASH WITH THE SYMMETRY MATE OF PART A. ADDITIONALLY, CHAIN D PART A DOES NOT CLASH WITH THE SYMMETRY MATE OF CHAIN D PART B. (4) SULFATES (SO4), (4S)-2-METHYL-2,4-PENTANEDIOLS (MPD), AND (4R)-2-METHYL-2,4-PENTANEDIOLS (MRD) FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. (5) ELECTRON DENSITY INDICATES THAT THE PEPTIDE BOND BETWEEN GLY 241 AND HIS 242 ON EACH SUBUNIT IS IN THE CIS CONFIGURATION.
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.83 Å2 / Biso mean: 27.854 Å2 / Biso min: 7.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→85.176 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 100 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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