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Yorodumi- PDB-4h09: Crystal structure of a leucine-rich repeat protein (EUBVEN_01088)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h09 | ||||||
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Title | Crystal structure of a leucine-rich repeat protein (EUBVEN_01088) from Eubacterium ventriosum ATCC 27560 at 2.50 A resolution | ||||||
Components | Hypothetical leucine rich repeat protein | ||||||
Keywords | PROTEIN BINDING / TWO LRR_5 DOMAINS / PF13306 FAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information CAP domain / CAP superfamily / Cysteine-rich secretory protein family / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) ...CAP domain / CAP superfamily / Cysteine-rich secretory protein family / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Fibronectin type III superfamily / Immunoglobulin-like fold / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Eubacterium ventriosum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a hypothetical leucine rich repeat protein (EUBVEN_01088) from Eubacterium ventriosum ATCC 27560 at 2.50 A resolution (CASP Target) 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 | 4h09.cif.gz | 715.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h09.ent.gz | 602.6 KB | Display | PDB format |
PDBx/mmJSON format | 4h09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/4h09 ftp://data.pdbj.org/pub/pdb/validation_reports/h0/4h09 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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5 |
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Unit cell |
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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 41579.320 Da / Num. of mol.: 5 / Fragment: UNP residues 33-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eubacterium ventriosum (bacteria) / Gene: EUBVEN_01088 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A5Z5V6 #2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 2.79 Å3/Da / Density % sol: 55.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1M sodium citrate pH 5.6, 20% 2-propanol, 20% polyethylene glycol 4000, 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: BL9-2 / Wavelength: 0.91837,0.97925 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 3, 2012 / Details: double crystal monochromator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→29.965 Å / Num. all: 78283 / Num. obs: 78283 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 56.569 Å2 / Rsym value: 0.09 / Net I/σ(I): 9.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 2.5→29.965 Å / Cor.coef. Fo:Fc: 0.9534 / Cor.coef. Fo:Fc free: 0.9344 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1). 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 ...Details: 1). 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. 2). POLYETHYLENE GLYCOL FRAGMENTS (PEG) FROM THE CRYSTALLIZATION BUFFER AND 1,2-ETHANEDIOL (EDO), USED AS A CRYOPROTECTANT, HAVE BEEN MODELED INTO THE STRUCTURE. 3). ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4). NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5). THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES.
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Displacement parameters | Biso max: 158.59 Å2 / Biso mean: 65.1717 Å2 / Biso min: 29.85 Å2
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Refine analyze | Luzzati coordinate error obs: 0.397 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.965 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 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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