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- PDB-1goy: HYDROLASE(ENDORIBONUCLEASE)RIBONUCLEASE BI(G SPECIFIC ENDONUCLEAS... -

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Basic information

Entry
Database: PDB / ID: 1goy
TitleHYDROLASE(ENDORIBONUCLEASE)RIBONUCLEASE BI(G SPECIFIC ENDONUCLEASE) (E.C.3.1.27.-) COMPLEXED WITH GUANOSINE-3'-PHOSPHATE (3'-GMP)
ComponentsRIBONUCLEASE
KeywordsHYDROLASE / ENDORIBONUCLEASE / NUCLEASE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region
Similarity search - Function
Barnase / Guanine-specific ribonuclease N1/T1/U2 / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-3'-MONOPHOSPHATE / Ribonuclease
Similarity search - Component
Biological speciesBACILLUS INTERMEDIUS (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsPolyakov, K.M. / Lebedev, A.A. / Pavlovsky, A.G. / Sanishvili, R.G. / Dodson, G.G.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The Structure of Substrate-Free Microbial Ribonuclease Binase and of its Complexes with 3'Gmp and Sulfate Ions
Authors: Polyakov, K.M. / Lebedev, A.A. / Okorokov, A.L. / Panov, K.I. / Schulga, A.A. / Pavlovsky, A.G. / Karpeisky, M.Y.A. / Dodson, G.G.
#1: Journal: Trends Biochem.Sci. / Year: 1990
Title: Comparison of Active Sites of Some Microbial Ribonucleases: Structural Basis for Guanylic Specificity
Authors: Sevcik, J. / Sanishvili, R.G. / Pavlovsky, A.G. / Polyakov, K.M.
#2: Journal: Kristallografiya(Russian) / Year: 1989
Title: The Crystall Structure of Bacterial Ribonuclease Binase
Authors: Pavlovsky, A.G. / Sanishvili, R.G. / Borisova, S.N. / Strokopytov, B.V. / Vagin, A.A. / Chepurnova, N.K. / Vainshtein, B.K.
#3: Journal: FEBS Lett. / Year: 1983
Title: Three-Dimensional Structure of Ribonuclese from Balillus Intermedius 7P at 3A Resolution
Authors: Pavlovsky, A.G. / Vagin, A.A. / Vainshtein, B.K. / Chepurnova, N.K. / Karpeisky, M.Y.
#4: Journal: Trends Biochem.Sci. / Year: 1983
Title: The Structural and Sequence Homology of Family of Microbial Ribonucleases
Authors: Hill, C. / Dodson, G. / Heinemann, U. / Saenger, W. / Mitsui, Y. / Nakamura, K. / Borisov, S. / Tischenko, G. / Polyakov, K. / Pavlovsky, S.
History
DepositionOct 26, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Advisory / Category: database_PDB_caveat
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE
B: RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6006
Polymers25,9492
Non-polymers6514
Water3,297183
1
A: RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4343
Polymers12,9741
Non-polymers4592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1673
Polymers12,9741
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)111.380, 69.560, 33.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RIBONUCLEASE / / BINASE / G SPECIFIC ENDONUCLEASE


Mass: 12974.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: MICROORGANISM / Source: (natural) BACILLUS INTERMEDIUS (bacteria) / References: UniProt: P00649, EC: 3.1.27.3
#2: Chemical ChemComp-3GP / GUANOSINE-3'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112-13 mg/mlprotein1drop
212 %PEG120001drop
325 mMphosphate1droppH7.0
43 %satammonium sulfate1drop
523-24 %PEG120001reservoir
650 mMglycerol1reservoirpH7.0

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: SYTNEX P21
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. obs: 14982 / % possible obs: 99 % / Redundancy: 2 %
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 24.9 Å / Num. obs: 15152 / % possible obs: 82.9 % / Num. measured all: 15152
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å / % possible obs: 34.2 % / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
BLANCphasing
CCP4phasing
REFMAC5.1.00refinement
RefinementMethod to determine structure: MIR / Resolution: 2→10 Å / Cor.coef. Fo:Fc: 0.951 / SU B: 3.682 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: NONE
Rfactor% reflectionSelection details
Rwork0.184 --
Rfree-0 %RANDOM
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 39 183 1940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0141.51066
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78321706
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6813743
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1764.5749
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.336 437
Rfree-0
Software
*PLUS
Name: REFMAC / Version: 5.1.00 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 24.9 Å / Rfactor obs: 0.184 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.2

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