[English] 日本語
Yorodumi
- PDB-3rv0: Crystal structure of K. polysporus Dcr1 without the C-terminal dsRBD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rv0
TitleCrystal structure of K. polysporus Dcr1 without the C-terminal dsRBD
ComponentsK. polysporus Dcr1
KeywordsRNA BINDING PROTEIN / RNase III enzyme
Function / homology
Function and homology information


ribonuclease III / ribonuclease III activity / rRNA processing / RNA binding / identical protein binding
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #260 / : / : / Dicers, N-terminal domain / Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #260 / : / : / Dicers, N-terminal domain / Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesVanderwaltozyma polyspora (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsNakanishi, K. / Weinberg, D.E. / Bartel, D.P. / Patel, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: The inside-out mechanism of dicers from budding yeasts.
Authors: Weinberg, D.E. / Nakanishi, K. / Patel, D.J. / Bartel, D.P.
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: K. polysporus Dcr1
B: K. polysporus Dcr1
C: K. polysporus Dcr1
D: K. polysporus Dcr1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,8018
Polymers157,7034
Non-polymers974
Water8,413467
1
A: K. polysporus Dcr1
B: K. polysporus Dcr1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9004
Polymers78,8522
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11920 Å2
ΔGint-117 kcal/mol
Surface area27920 Å2
MethodPISA
2
C: K. polysporus Dcr1
D: K. polysporus Dcr1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9004
Polymers78,8522
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-110 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.037, 112.974, 135.689
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
K. polysporus Dcr1


Mass: 39425.828 Da / Num. of mol.: 4 / Fragment: UNP residues 15-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vanderwaltozyma polyspora (fungus) / Strain: DSM 70294 / Gene: Kpol_455p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)rosetta2 / References: UniProt: A7TR32
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 180 mM Triammonium citrate, 20% PEG3350, 10 mM Na-HEPES buffer pH 7.5, vapor diffusion, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 69722 / % possible obs: 99.7 % / Redundancy: 10 % / Rsym value: 0.095 / Net I/σ(I): 27.3

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
DMphasing
PHENIXdev_538refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.29→43.41 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8584 / SU ML: 0.28 / σ(F): 0.32 / Phase error: 21.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 3303 5.09 %
Rwork0.1751 61579 -
obs0.1774 64882 92.38 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.823 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 267.97 Å2 / Biso mean: 45.9378 Å2 / Biso min: 4.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.6249 Å20 Å20 Å2
2--12.0558 Å2-0 Å2
3---1.6993 Å2
Refinement stepCycle: LAST / Resolution: 2.29→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8157 0 4 467 8628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018321
X-RAY DIFFRACTIONf_angle_d0.97411206
X-RAY DIFFRACTIONf_chiral_restr0.0671272
X-RAY DIFFRACTIONf_plane_restr0.0041426
X-RAY DIFFRACTIONf_dihedral_angle_d14.5423102
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.37460.27632720.20724851512374
2.3746-2.46970.22823110.18145660597186
2.4697-2.58210.2462990.19275859615889
2.5821-2.71820.26133280.18075993632191
2.7182-2.88840.22223540.17366147650193
2.8884-3.11140.24513180.18386313663195
3.1114-3.42440.25413030.19136580688398
3.4244-3.91960.23740.16336608698299
3.9196-4.93720.18973690.14776664703399
4.9372-43.4180.20893750.18516904727999
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)
10.3351-0.08060.14280.0721-0.07590.20770.0374-0.0009-0.2265-0.01640.07890.03670.1440.0028-0.04470.15620.0279-0.03820.09680.01910.1674-39.6435-21.33611.1765
20.1488-0.06010.14810.1004-0.03390.13790.0277-0.24960.04720.1810.0638-0.17290.00720.02610.01930.13280.0074-0.06010.2925-0.04260.184-26.4434-9.851625.5273
30.16420.0558-0.00690.01760.00330.0874-0.00520.0253-0.05110.0184-0.0074-0.04480.11980.1013-0.00730.10760.04990.01470.0674-0.01690.1038-32.8791-18.6287-0.708
40.14730.01840.05830.2629-0.07580.23670.0329-0.16930.03790.16330.05120.0212-0.0546-0.07480.05580.13420.00090.01280.1826-0.05790.1664-43.6485-3.194421.3012
50.0699-0.16230.04280.6851-0.12310.0487-0.15150.04510.00880.0620.03040.1194-0.2360.04860.00580.4646-0.0736-0.0640.16860.04560.2241-46.1203-37.901266.66
60.164-0.02390.15560.0649-0.05310.16580.1193-0.0077-0.1315-0.07240.08460.12710.1219-0.02210.15410.05050.0648-0.1377-0.00960.13030.1114-61.711-4.3855-26.0831
70.05470.04390.02190.09090.04650.09320.10430.2491-0.04-0.2169-0.03220.15180.05360.02020.07670.08740.0998-0.19030.26640.17360.0144-74.37225.922-51.1957
80.0460.00850.01020.0179-0.01640.04730.0213-0.0527-0.0636-0.00710.0560.14350.0485-0.04870.03710.1113-0.0677-0.03630.13880.21570.2179-68.0384-1.6147-24.2545
90.0755-0.03950.00660.117-0.03780.29330.10640.12850.0667-0.1630.09840.0122-0.05370.14610.27070.10380.0180.00360.18310.3289-0.0331-57.048813.9094-46.9924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 15:107))A0
2X-RAY DIFFRACTION2chain 'A' and ((resseq 108:260))A0
3X-RAY DIFFRACTION3chain 'B' and ((resseq 15:107))B0
4X-RAY DIFFRACTION4chain 'B' and ((resseq 108:257))B0
5X-RAY DIFFRACTION5chain 'B' and ((resseq 265:343))B0
6X-RAY DIFFRACTION6chain 'D' and ((resseq 15:107))D0
7X-RAY DIFFRACTION7chain 'D' and ((resseq 108:259))D0
8X-RAY DIFFRACTION8chain 'C' and ((resseq 15:107))C0
9X-RAY DIFFRACTION9chain 'C' and ((resseq 108:259))C0

+
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