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- PDB-3kd4: CRYSTAL STRUCTURE OF A PUTATIVE PROTEASE (BDI_1141) FROM PARABACT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kd4 | ||||||
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Title | CRYSTAL STRUCTURE OF A PUTATIVE PROTEASE (BDI_1141) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 2.00 A RESOLUTION | ||||||
![]() | Putative protease | ||||||
![]() | HYDROLASE / PUTATIVE PROTEASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | ![]() Jelly Rolls - #1130 / Immunoglobulin-like - #3140 / Domain of unknown function DUF3858 / Domain of unknown function DUF3857 / Domain of Unknown Function with PDB structure (DUF3857) / Domain of Unknown Function with PDB structure (DUF3858) / C8orf32 fold - #30 / C8orf32 fold / Jelly Rolls / Roll ...Jelly Rolls - #1130 / Immunoglobulin-like - #3140 / Domain of unknown function DUF3858 / Domain of unknown function DUF3857 / Domain of Unknown Function with PDB structure (DUF3857) / Domain of Unknown Function with PDB structure (DUF3858) / C8orf32 fold - #30 / C8orf32 fold / Jelly Rolls / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of Putative proteases (YP_001302526.1) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.2 KB | Display | ![]() |
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PDB format | ![]() | 190.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.5 KB | Display | ![]() |
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Full document | ![]() | 482.1 KB | Display | |
Data in XML | ![]() | 49.9 KB | Display | |
Data in CIF | ![]() | 76.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 55748.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_1141 / Plasmid: SpeedET / Production host: ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (RESIDUES 23-527) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 23-527) WAS EXPRESSED WITH A PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.28 Å3/Da / Density % sol: 71.27 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.67 | Details: 25.0000% Glycerol, 1.1000M ammonium dihydrogen phosphate, 0.1M citric acid pH 5.67, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 11, 2009 / 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→28.928 Å / Num. obs: 125591 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.142 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.59 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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 THE ...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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. PHOSPHATE (PO4) AND GLYCEROL (GOL) MODELED ARE PRESENT IN CRYSTLLIZATION/CRYO CONDITIONS.
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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 max: 75.58 Å2 / Biso mean: 25.486 Å2 / Biso min: 11.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2→28.928 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: 6314 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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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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