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Yorodumi- PDB-3kjk: Crystal structure of NMB1025, a member of YjgF protein family, fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kjk | ||||||
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Title | Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis (monoclinic crystal form) | ||||||
Components | NMB1025 protein | ||||||
Keywords | UNKNOWN FUNCTION / NMB1025 / YjgF protein family / Neisseria meningitidis / OPPF / Structural Genomics / Oxford Protein Production Facility | ||||||
Function / homology | Function and homology information RutC family, YoaB-like / RidA, conserved site / Uncharacterized protein family UPF0076 signature. / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Neisseria meningitidis serogroup B (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Ren, J. / Sainsbury, S. / Owens, R.J. / Oxford Protein Production Facility (OPPF) | ||||||
Citation | Journal: To be Published Title: Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis Authors: Ren, J. / Sainsbury, S. / Owens, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kjk.cif.gz | 287.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kjk.ent.gz | 235.5 KB | Display | PDB format |
PDBx/mmJSON format | 3kjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kjk_validation.pdf.gz | 517 KB | Display | wwPDB validaton report |
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Full document | 3kjk_full_validation.pdf.gz | 526.3 KB | Display | |
Data in XML | 3kjk_validation.xml.gz | 52.5 KB | Display | |
Data in CIF | 3kjk_validation.cif.gz | 73.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/3kjk ftp://data.pdbj.org/pub/pdb/validation_reports/kj/3kjk | HTTPS FTP |
-Related structure data
Related structure data | 3kjjSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 14426.478 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria) Strain: MC58 / Gene: NMB1025 / Plasmid: OPPF1359 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9JZJ4 #2: Water | ChemComp-HOH / | |
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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: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: di-Potassium Hydrogen Phosphate 1.2 M, Sodium di-Hydrogen Phosphate 0.6 M, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 24, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→30 Å / Num. obs: 69756 / % possible obs: 96.4 % / Observed criterion σ(I): -1.5 / Redundancy: 6.3 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.996 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6500 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KJJ Resolution: 2.29→30 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.871 / SU B: 16.451 / SU ML: 0.177 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.387 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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