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Yorodumi- PDB-4g2a: Crystal structure of a putative nutrient binding protein (lpg2210... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g2a | ||||||
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Title | Crystal structure of a putative nutrient binding protein (lpg2210) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.33 A resolution | ||||||
Components | hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / two domains protein / YARHG domain (PFAM13308) / DUF4424 (PF14415) / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1690 / Immunoglobulin-like - #3680 / Domain of unknown function DUF4424 / YARHG domain / YARHG domain superfamily / YARHG domain / Domain of unknown function (DUF4424) / YARHG / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1690 / Immunoglobulin-like - #3680 / Domain of unknown function DUF4424 / YARHG domain / YARHG domain superfamily / YARHG domain / Domain of unknown function (DUF4424) / YARHG / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.33 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a hypothetical protein (lpg2210) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.33 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 | 4g2a.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g2a.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 4g2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g2a_validation.pdf.gz | 438.5 KB | Display | wwPDB validaton report |
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Full document | 4g2a_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | 4g2a_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 4g2a_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/4g2a ftp://data.pdbj.org/pub/pdb/validation_reports/g2/4g2a | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37172.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria) Strain: Philadelphia 1 / Gene: lpg2210 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5ZTF2 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (29-349) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (29-349) WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 2.0M ammonium sulfate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794,0.9795,0.9184 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2012 Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.33→43.362 Å / Num. obs: 14552 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.44 % / Biso Wilson estimate: 43.761 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.09 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.33→43.362 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.9232 / Occupancy max: 1 / Occupancy min: 0.37 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. SO4 IONS MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS.
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Displacement parameters | Biso max: 124.1 Å2 / Biso mean: 42.4875 Å2 / Biso min: 10.18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.275 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→43.362 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.52 Å / Total num. of bins used: 7
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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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