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- PDB-3d5i: Crystal structure of ribonuclease Sa2 with exo-2',3'-cyclophospho... -

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Basic information

Entry
Database: PDB / ID: 3d5i
TitleCrystal structure of ribonuclease Sa2 with exo-2',3'-cyclophosphorotioate
ComponentsRibonuclease
KeywordsHYDROLASE / ribonuclease / mononucleotide / protein-mononucleotide complex / exo-2' / 3'-cyclophosphorotioate
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',3'-CYCLOPHOSPHOROTHIOATE / Ribonuclease
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBauerova-Hlinkova, V. / Sevcik, J.
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
DepositionMay 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)33,3767
Polymers32,7273
Non-polymers6494
Water3,045169
1
A: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1013
Polymers10,9091
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2702
Polymers10,9091
Non-polymers3611
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)101.221, 66.775, 57.070
Angle α, β, γ (deg.)90.00, 100.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-109-

HOH

21A-165-

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
Details: pEH200 was derived from pKK223-3 / Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Strain: R8/26 / Plasmid: pEH200 / Production host: Escherichia coli (E. coli) / Strain (production host): NovaBlue / References: UniProt: Q53752, EC: 3.1.4.8
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SGP / GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE


Mass: 361.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6PS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.89 Å3/Da / Density % sol: 57.5 %
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: Nov 15, 2001 / 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: 2.2→20 Å / Num. all: 19754 / Num. obs: 19754 / % possible obs: 90.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18
Reflection shellResolution: 2.2→2.257 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4.7 / Num. unique all: 579 / % possible all: 65.4

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Processing

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

1py3


Resolution: 2.2→19.94 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.902 / SU B: 11.228 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.279 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26237 913 5.1 %RANDOM
Rwork0.20756 ---
all0.2103 19754 --
obs0.2103 16896 93.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.761 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å2-0.04 Å2
2--2.56 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 38 169 2440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222339
X-RAY DIFFRACTIONr_bond_other_d0.0020.021618
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9723188
X-RAY DIFFRACTIONr_angle_other_deg1.7073.0033874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.86522.823124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30415346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7111525
X-RAY DIFFRACTIONr_chiral_restr0.1440.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022628
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02514
X-RAY DIFFRACTIONr_nbd_refined0.2070.2481
X-RAY DIFFRACTIONr_nbd_other0.2190.21723
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21095
X-RAY DIFFRACTIONr_nbtor_other0.0880.21182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2156
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.28
X-RAY DIFFRACTIONr_mcbond_it0.8051.51749
X-RAY DIFFRACTIONr_mcbond_other0.131.5561
X-RAY DIFFRACTIONr_mcangle_it0.95322243
X-RAY DIFFRACTIONr_scbond_it1.60731152
X-RAY DIFFRACTIONr_scangle_it2.4344.5945
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 45 -
Rwork0.229 1052 -
obs-579 78.08 %
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)
11.4521.3244-0.29793.7635-0.63992.54460.04260.0458-0.0690.0608-0.05160.1552-0.15370.37640.0090.0385-0.03740.02380.0705-0.0084-0.018765.9747-1.7064-26.5082
22.0196-0.5467-0.98651.69650.76063.0087-0.0147-0.40950.03110.20020.04560.0344-0.02490.2003-0.03090.0852-0.04850.00540.08250.00550.022459.995-1.59-14.2669
332.728721.8428-19.174235.1654-3.247415.6626-2.22081.788-0.29251.13732.1349-3.17570.6778-0.46030.08580.0050.025-0.12930.34040.03670.170378.1359-6.7073-19.3622
41.63560.0033-0.73621.16580.46332.21160.0264-0.07890.2324-0.0827-0.0249-0.0326-0.43740.1712-0.00160.0715-0.05880.01370.0916-0.00090.025163.42433.5787-20.665
57.3459-0.78582.94951.5923-0.72754.0373-0.06810.3211-0.1336-0.14540.08210.16320.4503-0.1735-0.0140.05190.03630.03840.0150.02190.025462.8832-24.324813.6041
63.8333-1.26142.41595.2251.89076.9522-0.0315-0.5533-0.37240.57630.05840.28430.3716-0.1382-0.02690.01860.06130.03640.05850.06770.003662.9215-20.865125.9962
716.634618.610516.071626.023712.677620.93290.6778-2.3389-1.39481.2767-1.89870.58390.9252-2.54661.2209-0.0315-0.04290.14560.3661-0.14970.293253.7863-36.351721.0971
82.4618-1.11880.77842.42610.96742.35010.07540.0895-0.322-0.0051-0.08290.08410.25680.13390.0075-0.00880.04130.02060.0690.01580.059866.8576-24.53118.313
94.7781-1.19220.46191.722-0.27265.2520.03620.17640.22060.0733-0.0191-0.291-0.16130.5155-0.0171-0.0347-0.0221-0.01670.10770.04120.016969.263-6.7112.1602
107.4868-1.1577-5.61410.5259-4.668111.60990.36030.39760.5123-0.6499-0.2618-0.0659-0.4668-0.1012-0.09840.03350.0606-0.01980.12570.0159-0.041554.6652-1.744311.6948
113.0362-0.4518-0.65531.39060.9055.82560.18970.31790.0951-0.0814-0.28480.004-0.4183-0.45340.0951-0.01430.07940.00960.19080.0154-0.024860.4824-8.00052.3799
1211.8187-4.81654.00573.993-4.456613.83060.54640.5523-0.1531-0.0221-0.3539-0.1492-0.20030.1951-0.1926-0.03860.01030.00820.12680.0262-0.028669.6987-7.79363.6893
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 344 - 34
2X-RAY DIFFRACTION2AA35 - 6135 - 61
3X-RAY DIFFRACTION3AA62 - 6862 - 68
4X-RAY DIFFRACTION4AA69 - 9769 - 97
5X-RAY DIFFRACTION5BB1 - 301 - 30
6X-RAY DIFFRACTION6BB31 - 6031 - 60
7X-RAY DIFFRACTION7BB61 - 6861 - 68
8X-RAY DIFFRACTION8BB69 - 9769 - 97
9X-RAY DIFFRACTION9CC5 - 265 - 26
10X-RAY DIFFRACTION10CC27 - 3427 - 34
11X-RAY DIFFRACTION11CC35 - 8135 - 81
12X-RAY DIFFRACTION12CC82 - 9782 - 97

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