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- PDB-3dgy: Crystal structure of ribonuclease Sa2 with guanosine-2'-cyclophosphate -

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Basic information

Entry
Database: PDB / ID: 3dgy
TitleCrystal structure of ribonuclease Sa2 with guanosine-2'-cyclophosphate
ComponentsRibonuclease
KeywordsHYDROLASE / ribonuclease / protein-mononucleotide complex / guanosine-2'-monophosphate / mononucleotide
Function / homology
Function and homology information


: / RNA endonuclease activity / RNA binding
Similarity search - Function
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-2'-MONOPHOSPHATE / beta-D-glucopyranose / Ribonuclease
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSevcik, J. / Bauerova-Hlinkova, V.
CitationJournal: Febs J. / Year: 2009
Title: Structure of RNase Sa2 complexes with mononucleotides - new aspects of catalytic reaction and substrate recognition
Authors: Bauerova-Hlinkova, V. / Dvorsky, R. / Perecko, D. / Povazanec, F. / Sevcik, J.
History
DepositionJun 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease
B: Ribonuclease
C: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5598
Polymers32,7273
Non-polymers8325
Water4,990277
1
A: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1853
Polymers10,9091
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3683
Polymers10,9091
Non-polymers4592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0052
Polymers10,9091
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.489, 67.313, 57.234
Angle α, β, γ (deg.)90.00, 100.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

21A-220-

HOH

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Components

#1: Protein Ribonuclease / / ribonuclease Sa2


Mass: 10909.012 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Strain: R8/26 / Plasmid: pEH200 / Production host: Escherichia coli (E. coli) / Strain (production host): Nova Blue / References: UniProt: Q53752, EC: 3.1.4.8
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-2GP / GUANOSINE-2'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: ammonium sulfate, phosphate buffer pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 15, 2003 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 35195 / Num. obs: 34762 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.3
Reflection shellResolution: 1.8→1.82 Å / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1104 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1py3

1py3


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.295 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24635 1750 5 %RANDOM
Rwork0.21548 ---
obs0.21707 33012 98.78 %-
all-34762 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.922 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20.16 Å2
2--2.28 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 51 277 2545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222336
X-RAY DIFFRACTIONr_bond_other_d0.0020.021619
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9793181
X-RAY DIFFRACTIONr_angle_other_deg0.9313.0033875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.78522.705122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92215346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4161525
X-RAY DIFFRACTIONr_chiral_restr0.080.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
X-RAY DIFFRACTIONr_nbd_refined0.210.2464
X-RAY DIFFRACTIONr_nbd_other0.210.21695
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21108
X-RAY DIFFRACTIONr_nbtor_other0.0790.21181
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2180
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2040.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.221
X-RAY DIFFRACTIONr_mcbond_it0.8091.51733
X-RAY DIFFRACTIONr_mcbond_other0.1761.5555
X-RAY DIFFRACTIONr_mcangle_it0.98622223
X-RAY DIFFRACTIONr_scbond_it1.66731157
X-RAY DIFFRACTIONr_scangle_it2.3894.5958
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 110 -
Rwork0.242 2434 -
obs--97.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8264-1.0157-3.00546.13420.8765.47180.23770.06420.39060.016-0.09890.2261-0.85940.5166-0.13880.0757-0.13680.0177-0.1392-0.0116-0.035467.0556-3.7823-26.7731
22.3266-0.5894-0.51980.89050.42632.5950.0236-0.1757-0.07360.1128-0.03840.0333-0.0520.19360.01480.0235-0.03910.0073-0.0731-0.00080.010562.2561-15.7888-18.8526
35.27361.29950.92341.60370.12452.86350.2232-0.0425-0.34920.1072-0.0533-0.2138-0.14540.3995-0.16990.0266-0.06470.0021-0.0441-0.01390.005566.5854-11.1994-18.6462
45.9241-5.59639.54927.2201-3.45931.39040.4271-0.1602-0.0415-0.3803-0.25760.7134-1.0108-1.5079-0.16950.1552-0.03030.0132-0.11660.0214-0.029360.2174-2.402-28.6953
59.1713-1.72581.66541.7448-0.88932.65420.03530.5452-0.2078-0.0714-0.05230.09860.5775-0.08980.017-0.00040.0510.04-0.07630.0093-0.056666.0059-37.356413.1487
69.4862-0.98451.710217.8156-17.750717.7423-0.05530.4723-0.22210.27460.36851.07050.3455-1.07-0.3132-0.1391-0.03440.0865-0.0045-0.020.115651.4088-33.575119.6782
75.7715-1.4256-0.40743.43420.91672.5666-0.2417-0.6542-0.23660.50560.1042-0.06210.16620.25050.1374-0.02260.06340.0215-0.02170.0431-0.053165.6688-31.266527.0567
82.64450.17920.05622.2963-0.56353.4872-0.0917-0.107-0.352-0.0086-0.11590.11490.43570.06430.2076-0.02860.05190.0576-0.07370.0260.040265.0414-38.158118.7274
97.0319-1.374-0.85291.9461-0.23862.91580.03750.28290.11720.0987-0.257-0.2341-0.3240.13210.2195-0.05790.0288-0.02660.00180.0528-0.067464.3258-17.073711.6113
100.73531.55410.52636.5556-2.45356.78510.05590.0945-0.1982-0.5652-0.5030.36820.1725-0.70.4472-0.10990.0907-0.00720.2045-0.0824-0.060359.1627-24.5436-3.9522
113.98190.4106-0.60424.7170.38635.14650.27560.36530.23170.1046-0.4288-0.1538-0.4532-0.18380.1532-0.05590.0766-0.00540.04920.0347-0.054762.9896-17.90315.866
1211.11-5.35524.08613.0566-1.375911.86040.39090.5776-0.5801-0.0112-0.31290.0066-0.40670.2572-0.078-0.12660.04330.03740.04120.0753-0.03169.9765-19.9963.4564
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 164 - 16
2X-RAY DIFFRACTION2AA17 - 6117 - 61
3X-RAY DIFFRACTION3AA62 - 9162 - 91
4X-RAY DIFFRACTION4AA92 - 9792 - 97
5X-RAY DIFFRACTION5BB1 - 251 - 25
6X-RAY DIFFRACTION6BB26 - 3426 - 34
7X-RAY DIFFRACTION7BB35 - 5835 - 58
8X-RAY DIFFRACTION8BB59 - 9759 - 97
9X-RAY DIFFRACTION9CC5 - 375 - 37
10X-RAY DIFFRACTION10CC38 - 5338 - 53
11X-RAY DIFFRACTION11CC54 - 8254 - 82
12X-RAY DIFFRACTION12CC83 - 9783 - 97

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