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- PDB-1gou: Ribonuclease Binase (G Specific Endonuclease) Unliganded Form -

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Basic information

Entry
Database: PDB / ID: 1gou
TitleRibonuclease Binase (G Specific Endonuclease) Unliganded Form
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 / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesBACILLUS INTERMEDIUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPolyakov, K.M. / Lebedev, A.A. / Dodson, G.G.
CitationJournal: 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.
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 1.3May 30, 2018Group: Data collection / Structure summary / Category: diffrn_source / struct / Item: _diffrn_source.pdbx_synchrotron_site / _struct.title
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6May 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


Theoretical massNumber of molelcules
Total (without water)25,9492
Polymers25,9492
Non-polymers00
Water4,594255
1
A: RIBONUCLEASE


Theoretical massNumber of molelcules
Total (without water)12,9741
Polymers12,9741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RIBONUCLEASE


Theoretical massNumber of molelcules
Total (without water)12,9741
Polymers12,9741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)115.030, 33.290, 78.700
Angle α, β, γ (deg.)90.00, 119.08, 90.00
Int Tables number5
Space group name H-MC121

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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 genetically manipulated source
Details: UNLIGANDED FORM / Source: (gene. exp.) BACILLUS INTERMEDIUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00649, EC: 3.1.27.3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growpH: 9 / Details: pH 9.00
Crystal grow
*PLUS
pH: 7 / 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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Type: EMBL/DESY, HAMBURG / Wavelength: 0.98
DetectorDetails: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→10 Å / Num. obs: 28989 / % possible obs: 96.3 % / Redundancy: 4 %
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 30591 / % possible obs: 96 % / Num. measured all: 95418 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 1.69 Å / % possible obs: 94.1 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 7.3

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Processing

Software
NameVersionClassification
REFMAC5.1.00refinement
DENZOdata reduction
SCALEPACKdata scaling
BLANCphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→10 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.39 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.176 1546 5.1 %RANDOM
Rwork0.14 ---
obs-28989 96.3 %-
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: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 0 255 1981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211816
X-RAY DIFFRACTIONr_bond_other_d0.0030.021625
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg2.0771.9292465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg2.55533741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1490.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022074
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02434
X-RAY DIFFRACTIONr_nbd_refined0.1890.1276
X-RAY DIFFRACTIONr_nbd_other0.1540.11477
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.11039
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.1121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.15
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.118
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.123
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8221.51103
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.77121768
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2693713
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8034.5697
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: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.175 114
Rwork0.144 2029
Software
*PLUS
Name: REFMAC / Version: 5.1.00 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.14 / Rfactor Rfree: 0.176 / Rfactor Rwork: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1

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