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- PDB-3hrp: Crystal structure of Structural genomics protein of unknown funct... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hrp | ||||||
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Title | Crystal structure of Structural genomics protein of unknown function (NP_812590.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.70 A resolution | ||||||
![]() | Uncharacterized protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NP_812590.1 / Structural genomics protein of unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | ![]() TolB, C-terminal domain / IPT/TIG domain / Six-bladed beta-propeller, TolB-like / IPT domain / 6 Propeller / Neuraminidase / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...TolB, C-terminal domain / IPT/TIG domain / Six-bladed beta-propeller, TolB-like / IPT domain / 6 Propeller / Neuraminidase / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of Structural genomics protein of unknown function (NP_812590.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.70 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 | ![]() | 102 KB | Display | ![]() |
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PDB format | ![]() | 79 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.9 KB | Display | ![]() |
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Full document | ![]() | 451 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 30.3 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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Unit cell |
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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY PROVIDES SUPPORTING EVIDENCE THAT THE MONOMER IS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION |
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Components
#1: Protein | Mass: 45277.516 Da / Num. of mol.: 1 / Fragment: sequence database residues 23-430 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BT_3679, NP_812590.1 / Plasmid: SpeedET / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-MPD / ( | ||||
#3: Chemical | ChemComp-EDO / #4: 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 | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.58 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND . Crystal grow | Temperature: 277 K / pH: 7.64 | Details: 32.0000% 2-methyl-2,4-pentanediol, 0.2000M magnesium chloride, 0.1M Imidazole pH 7.64, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MAR MAR325 / Detector: CCD / Date: Feb 19, 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: 1.7→29.49 Å / Num. obs: 45480 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.05 % / Biso Wilson estimate: 16.64 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.78 | ||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 1.5 / % possible all: 93 |
-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. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. A MPD PLUS 15 EDO'S FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE STRUCTURE. 5. 8 N-TERMINAL RESIDUES WITHIN THE STRUCTURE ARE DISODERED. 6. ADDITIONAL DENSITY ADJACENT TO GLU76 WAS MODELED AS 2 WATERS BUT COULD ALSO BE DUE TO POSTTRANSLATIONAL MODIFICATION OF THAT RESIDUE.
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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 mean: 7.85 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 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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