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- PDB-2a2l: Crystal structure of Klebsiella pneumoniae protein ORFY, Pfam DUF336 -
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Open data
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Basic information
Entry | Database: PDB / ID: 2a2l | ||||||
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Title | Crystal structure of Klebsiella pneumoniae protein ORFY, Pfam DUF336 | ||||||
![]() | unknown | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramagopal, U. / Patskovsky, Y. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125 KB | Display | ![]() |
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PDB format | ![]() | 99.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.9 KB | Display | ![]() |
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Full document | ![]() | 458.7 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 42.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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. |
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Components
#1: Protein | Mass: 15352.450 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine 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: 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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