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Yorodumi- PDB-3hl1: CRYSTAL STRUCTURE OF A FERRITIN LIKE PROTEIN (CC_0557) FROM CAULO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hl1 | ||||||
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Title | CRYSTAL STRUCTURE OF A FERRITIN LIKE PROTEIN (CC_0557) FROM CAULOBACTER VIBRIOIDES AT 1.95 A RESOLUTION | ||||||
Components | Ferritin like protein | ||||||
Keywords | METAL BINDING PROTEIN / FERRITIN-LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | Function and homology information Helix Hairpins - #1530 / Iminophenyl-pyruvate dimer synthase / Ferritin-like / Helix Hairpins / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Helix non-globular / Special / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Caulobacter vibrioides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of ferritin like protein from Caulobacter crescentus CB15 (NP_419375.1) from Caulobacter crescentus at 1.95 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 | 3hl1.cif.gz | 126.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hl1.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/3hl1 ftp://data.pdbj.org/pub/pdb/validation_reports/hl/3hl1 | 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 35480.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Strain: CB15 / Gene: CC_0557, NP_419375.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9AAP0 #2: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #3: 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 | |
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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: 2.01 Å3/Da / Density % sol: 38.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.93 Details: 17.5000% polyethylene glycol 6000, 0.1M citric acid pH 4.93, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97876,0.97828 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 22, 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: 1.95→29.424 Å / Num. obs: 41306 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.88 % / Biso Wilson estimate: 31.69 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 12.61 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.95→29.424 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 7.913 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.161 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. THE B CHAIN IS SEVERELY DISORDERED. THE MODEL FOR B CHAIN WAS BUILT BASED ON THE CHAIN A WHERE DENSITY IS NOT DEFINITE. ADDITIONALLY, A291-297 HAS POOR DENSITY. 5. AN UNKNOWN LIGAND (UNL) IS MODELED FOR EACH MONOMER IN A SITE WHERE RESIDUES ARE HIGHLY CONSERVED.
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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: 84.06 Å2 / Biso mean: 39.863 Å2 / Biso min: 14.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→29.424 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 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.95→2.001 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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