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Yorodumi- PDB-2a2l: Crystal structure of Klebsiella pneumoniae protein ORFY, Pfam DUF336 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a2l | ||||||
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Title | Crystal structure of Klebsiella pneumoniae protein ORFY, Pfam DUF336 | ||||||
Components | unknown | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / UNKNOWN / PSI / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Haem-degrading domain / Corrinoid adenosyltransferase PduO/GlcC-like / Corrinoid adenosyltransferase PduO/GlcC-like superfamily / Haem degrading protein HbpS-like / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Ramagopal, U. / Patskovsky, Y. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Klebsiella Pneumoniae Hypothetical Protein Orfy Authors: Ramagopal, U. / Patskovsky, Y. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a2l.cif.gz | 125 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a2l.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 2a2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a2l_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 2a2l_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 2a2l_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 2a2l_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/2a2l ftp://data.pdbj.org/pub/pdb/validation_reports/a2/2a2l | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 4 - 146 / Label seq-ID: 3 - 145
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Details | The assymetric unit contains tetramer (A,B,C,D), but the biological assembly is an octamer. The symmetry related second tetramer is generated be the two-fold axis -x+1, -y+1, z. |
-Components
#1: Protein | Mass: 15352.450 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ORFY / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q48422 #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: 2.48 Å3/Da / Density % sol: 50.09 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% MPD, 0.1M HEPES, 0.2M Sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 87 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.989 / Wavelength: 0.989 Å |
Detector | Type: ADSC QUANTAM Q315 / Detector: CCD / Date: Mar 7, 2005 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.989 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 33912 / Num. obs: 32826 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.5 / Redundancy: 9.2 % / Rmerge(I) obs: 0.122 / Rsym value: 0.118 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2765 / Rsym value: 0.222 / % possible all: 79.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→103.69 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.812 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.333 / ESU R Free: 0.274 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.415 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→103.69 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1059 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 20
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