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Yorodumi- PDB-3db7: Crystal structure of a putative calcium-regulated periplasmic pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3db7 | ||||||
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Title | Crystal structure of a putative calcium-regulated periplasmic protein (bt0923) from bacteroides thetaiotaomicron at 1.40 A resolution | ||||||
Components | putative calcium-regulated periplasmic protein | ||||||
Keywords | Ca-BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Inhibitor of vertebrate lysozyme, Ivy - #30 / Putative beta-lactamase-inhibitor-like, PepSY-like / Putative beta-lactamase-inhibitor-like, PepSY-like / Inhibitor of vertebrate lysozyme, Ivy / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Putative periplasmic protein Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of putative calcium-regulated periplasmic protein of unknown function (NP_809836.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.40 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 | 3db7.cif.gz | 45.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3db7.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 3db7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3db7_validation.pdf.gz | 427.8 KB | Display | wwPDB validaton report |
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Full document | 3db7_full_validation.pdf.gz | 428.2 KB | Display | |
Data in XML | 3db7_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 3db7_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/3db7 ftp://data.pdbj.org/pub/pdb/validation_reports/db/3db7 | 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | AUTHORS STATE THAT ONLY WHEN CA1 AND CA2 ARE INCLUDED IN THE CALCULATION, DOES PISA (v1.14) PREDICT THAT A STABLE DIMER COULD BE A PROBABLE QUATERNARY STRUCTURE. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING (SEC+SLS) WITHOUT ADDED CALCIUM SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. WHEN A SAMPLE WAS RUN WITH 0.2 M CALCIUM CHLORIDE IN THE MOBILE PHASE (SIMILAR CONCENTRATION TO THAT IN THE CRYSTALLIZATION REAGENT), THE SEC+SLS RESULTS SHOWED PRIMARILY DIMER. |
-Components
#1: Protein | Mass: 14790.481 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: NP_809836.1, BT_0923 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A994 | ||||||
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#2: Chemical | #3: Chemical | #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 0.2000M CaAcetate, 20.0000% PEG-3350, No Buffer pH 7., NANODROP, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97947,0.97891 | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 4, 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: 1.4→24.922 Å / Num. obs: 23150 / % possible obs: 90.5 % / Observed criterion σ(I): -3 / Redundancy: 2.149 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.44 | ||||||||||||||||||||||||||||||||||||||||||||
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: 1.4→24.922 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.134 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.071 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.ETHYLENE GLYCOL AND CALCIUM IONS FROM THE CRYSTALLIZATION COND ARE MODELED IN THIS STRUCTURE.
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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: 10.575 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→24.922 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.437 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 5.4168 Å / Origin y: 48.0223 Å / Origin z: 9.8704 Å
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