[English] 日本語
Yorodumi
- PDB-3d5i: Crystal structure of ribonuclease Sa2 with exo-2',3'-cyclophospho... -

+
Open data


ID or keywords:

Loading...

-
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
Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more