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- PDB-2j4t: Biological and Structural Features of Murine Angiogenin-4, an Ang... -

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Basic information

Entry
Database: PDB / ID: 2j4t
TitleBiological and Structural Features of Murine Angiogenin-4, an Angiogenic Protein
ComponentsANGIOGENIN-4
KeywordsHYDROLASE / ANGIOGENESIS / ENDONUCLEASE / DIFFERENTIATION / CANCER / NUCLEASE / RIBONUCLEASE / DEVELOPMENTAL PROTEIN / PROTEIN SYNTHESIS INHIBITOR / PYRROLIDONE CARBOXYLIC ACID
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / RNA nuclease activity / secretory granule / response to bacterium / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / angiogenesis / endonuclease activity / nucleic acid binding ...Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / RNA nuclease activity / secretory granule / response to bacterium / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / angiogenesis / endonuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / positive regulation of cell population proliferation / nucleolus / extracellular space
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Angiogenin-4 / Angiogenin-4
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsCrabtree, B. / Holloway, D.E. / Baker, M.D. / Acharya, K.R. / Subramanian, V.
CitationJournal: Biochemistry / Year: 2007
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
DepositionSep 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANGIOGENIN-4
B: ANGIOGENIN-4


Theoretical massNumber of molelcules
Total (without water)33,1562
Polymers33,1562
Non-polymers00
Water1,36976
1
A: ANGIOGENIN-4


Theoretical massNumber of molelcules
Total (without water)16,5781
Polymers16,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ANGIOGENIN-4


Theoretical massNumber of molelcules
Total (without water)16,5781
Polymers16,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)97.472, 31.422, 95.471
Angle α, β, γ (deg.)90.00, 118.85, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.84183, 0.53951, -0.01558), (0.53585, -0.83888, -0.09567), (-0.06468, 0.07219, -0.99529)
Vector: 23.5868, 11.43896, 39.91283)

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Components

#1: Protein ANGIOGENIN-4 / MOUSE ANGIOGENIN-4


Mass: 16578.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q80Z85, UniProt: Q3TMQ6*PLUS, EC: 3.1.27.5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38 %
Crystal growpH: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BWK

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
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1035 6.1 %RANDOM
Rwork0.229 ---
obs0.229 12698 74.4 %-
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1--2.457 Å20 Å2-8.504 Å2
2--19.055 Å20 Å2
3----16.598 Å2
Refinement stepCycle: LAST / Resolution: 2.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 0 76 2001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.02→2.11 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.37 -6.1 %
Rwork0.3292 994 -
obs--49.1 %

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