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- PDB-2j4t: Biological and Structural Features of Murine Angiogenin-4, an Ang... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2j4t | ||||||
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Title | Biological and Structural Features of Murine Angiogenin-4, an Angiogenic Protein | ||||||
![]() | ANGIOGENIN-4 | ||||||
![]() | HYDROLASE / ANGIOGENESIS / ENDONUCLEASE / DIFFERENTIATION / CANCER / NUCLEASE / RIBONUCLEASE / DEVELOPMENTAL PROTEIN / PROTEIN SYNTHESIS INHIBITOR / PYRROLIDONE CARBOXYLIC ACID | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / RNA nuclease activity / secretory granule / response to bacterium / antibacterial humoral response / endonuclease activity / angiogenesis / nucleic acid binding / defense response to bacterium ...Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / RNA nuclease activity / secretory granule / response to bacterium / antibacterial humoral response / endonuclease activity / angiogenesis / nucleic acid binding / defense response to bacterium / positive regulation of cell population proliferation / nucleolus / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Crabtree, B. / Holloway, D.E. / Baker, M.D. / Acharya, K.R. / Subramanian, V. | ||||||
![]() | ![]() Title: Biological and Structural Features of Murine Angiogenin-4, an Angiogenic Protein Authors: Crabtree, B. / Holloway, D.E. / Baker, M.D. / Acharya, K.R. / Subramanian, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62 KB | Display | ![]() |
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PDB format | ![]() | 44.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.5 KB | Display | ![]() |
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Full document | ![]() | 442.7 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bwkS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.84183, 0.53951, -0.01558), Vector: |
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Components
#1: Protein | Mass: 16578.154 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q80Z85, UniProt: Q3TMQ6*PLUS, EC: 3.1.27.5 #2: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38 % |
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Crystal grow | pH: 8.5 Details: INITIAL, TWINNED CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (8 MG ML IN WATER) AND RESERVOIR (25 % PEG 3350, 0.2 M LI2SO4, 0.1 M TRIS-HCL, PH 8.5). THESE CRYSTALS WERE ...Details: INITIAL, TWINNED CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (8 MG ML IN WATER) AND RESERVOIR (25 % PEG 3350, 0.2 M LI2SO4, 0.1 M TRIS-HCL, PH 8.5). THESE CRYSTALS WERE USED TO SEED PREEQUILIBRATED DROPS CONTAINING 4 MG ML PROTEIN, 20 % PEG 3350, 0.05 M LI2SO4, 0.09 M TRIS-HCL, PH 8.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. obs: 17076 / % possible obs: 74.2 % / Observed criterion σ(I): 2 / Redundancy: 2.08 % / Biso Wilson estimate: 26.471 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 0.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.8 / % possible all: 49.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BWK Resolution: 2.02→50 Å / Rfactor Rfree error: 0.00923 / Cross valid method: THROUGHOUT / σ(F): 2 Details: RESIDUES A1, A3, A50, A87, A96, B1, B53, B58, B59 TRUNCATED TO ALA DUE TO POOR DENSITY
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Displacement parameters | Biso mean: 39 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.02→2.11 Å / Total num. of bins used: 8
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