[English] 日本語
Yorodumi
- PDB-4khy: Ternary complex of rb69 mutant L415F with ribonucleotide at -3 po... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4khy
TitleTernary complex of rb69 mutant L415F with ribonucleotide at -3 position
Components
  • DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3')
  • DNA polymerase
  • DNA/RNA (5'-D(*AP*CP*AP*GP*G)-R(P*U)-D(P*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
KeywordsTRANSFERASE/DNA / RIBONUCLEOTIDE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase ...DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsClausen, A.R. / Pedersen, L.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
Authors: Clausen, A.R. / Murray, M.S. / Passer, A.R. / Pedersen, L.C. / Kunkel, T.A.
History
DepositionMay 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 20, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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_ref_seq_dif.details / _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: DNA polymerase
T: DNA/RNA (5'-D(*AP*CP*AP*GP*G)-R(P*U)-D(P*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
P: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,35916
Polymers114,4993
Non-polymers86113
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-125 kcal/mol
Surface area41760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.795, 118.240, 127.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / DNA/RNA hybrid / DNA chain , 3 types, 3 molecules ATP

#1: Protein DNA polymerase / / Gp43


Mass: 104689.156 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q38087, DNA-directed DNA polymerase
#2: DNA/RNA hybrid DNA/RNA (5'-D(*AP*CP*AP*GP*G)-R(P*U)-D(P*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')


Mass: 5552.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TEMPLATE STRAND
#3: DNA chain DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3')


Mass: 4256.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PRIMER STRAND

-
Non-polymers , 4 types, 493 molecules

#4: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 50 MM TRIS-HCL, 17.5% PEG350, 180 MM CALCIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K, temperature 298K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 23, 2011
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 50172 / % possible obs: 98.4 % / Observed criterion σ(I): 2.9
Reflection shellResolution: 2.2→2.33 Å / % possible all: 88.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(PHENIX.REFINE: 1.7_650)model building
PHENIX(PHENIX.REFINE: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CQ8
Resolution: 2.25→22.34 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 2491 4.96 %
Rwork0.198 --
obs0.201 50172 85.4 %
all-50172 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.15 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6092 Å2-0 Å20 Å2
2---0.9988 Å20 Å2
3---4.608 Å2
Refinement stepCycle: LAST / Resolution: 2.25→22.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7203 649 41 480 8373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078329
X-RAY DIFFRACTIONf_angle_d0.80511472
X-RAY DIFFRACTIONf_dihedral_angle_d11.4332795
X-RAY DIFFRACTIONf_chiral_restr0.0531214
X-RAY DIFFRACTIONf_plane_restr0.0031376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.248-2.29160.33241050.26732105X-RAY DIFFRACTION69
2.2916-2.33830.38031250.24692417X-RAY DIFFRACTION79
2.3383-2.38910.31951460.25172473X-RAY DIFFRACTION81
2.3891-2.44460.361100.26532326X-RAY DIFFRACTION75
2.4446-2.50570.33271110.2672374X-RAY DIFFRACTION77
2.5057-2.57340.36361340.27132369X-RAY DIFFRACTION77
2.5734-2.6490.29471400.26642392X-RAY DIFFRACTION79
2.649-2.73430.37411290.26762351X-RAY DIFFRACTION77
2.7343-2.83190.27811290.26872312X-RAY DIFFRACTION76
2.8319-2.9450.29411210.25552420X-RAY DIFFRACTION78
2.945-3.07870.25961260.23582576X-RAY DIFFRACTION83
3.0787-3.24060.28511350.22842946X-RAY DIFFRACTION95
3.2406-3.44290.23131730.20633077X-RAY DIFFRACTION100
3.4429-3.70760.23891620.18723117X-RAY DIFFRACTION100
3.7076-4.07870.19721530.16013025X-RAY DIFFRACTION96
4.0787-4.66420.16691630.13463015X-RAY DIFFRACTION97
4.6642-5.85890.19461760.15033092X-RAY DIFFRACTION97
5.8589-22.34630.21811530.18743294X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.14840.1756-0.04430.241-0.01540.04430.05940.00440.16060-0.055-0.2941-0.04540.03860.0150.1818-0.00620.03650.17040.04620.510928.80660.646233.3393
20.1872-0.0278-0.07470.47150.3350.461-0.03260.0051-0.06660.3588-0.1268-0.16190.14770.02740.02110.2993-0.0179-0.05890.19210.00240.214112.133333.229354.8009
30.15280.0534-0.02840.34760.04220.15850.0427-0.13350.0707-0.004-0.0623-0.1276-0.0329-0.03250.0020.1976-0.0046-0.03070.2060.01110.20728.348643.663743.8908
40.2989-0.0172-0.16920.06480.02090.09760.03490.01880.00950.0199-0.00280.0184-0.0554-0.0459-0.00630.4505-0.06790.03410.2571-0.01470.1994-0.031426.092856.3054
50.1574-0.04390.07610.06210.04170.29790.13160.06560.1369-0.10260.1097-0.22480.19150.04820.35030.0694-0.01450.0885-0.08090.2768-0.16277.636253.972118.2183
60.3908-0.0520.14950.06120.0740.21690.14340.1808-0.1863-0.0177-0.0932-0.01960.43140.0958-0.00240.6960.13990.05320.2972-0.03830.328310.110527.014415.5318
70.2565-0.09150.05230.105-0.00030.06110.05790.32840.1032-0.4202-0.023-0.01850.2770.06060.02330.51430.02360.00280.2950.04650.0472-0.680445.45057.0578
80.1869-0.29620.01830.4840.03460.43240.02430.0391-0.162-0.2440.01110.27630.15710.0211-0.02950.3464-0.0311-0.07610.14870.00620.1931-15.029833.190316.6595
90.7158-0.1271-0.16820.6674-0.12220.1034-0.1321-0.4858-0.05850.23630.11460.1762-0.0217-0.1036-0.00620.25480.03560.02570.37150.04660.2466-19.826441.43146.0953
100.0737-0.0256-0.02220.0415-0.01360.2273-0.0539-0.0524-0.1206-0.0541-0.08540.0691-0.0361-0.02690.01350.3311-0.0766-0.07870.40370.13670.4558-31.766534.935624.889
110.28630.0481-0.01740.01220.00380.015-0.01650.041-0.0111-0.0185-0.04020.01780.0218-0.08260.03340.2695-0.01290.1070.87360.10281.0031-34.018258.253529.4602
120.0829-0.05860.06720.0431-0.04540.06570.0070.0530.04890.0209-0.0375-0.0264-0.00880.01180.01610.14840.0215-0.04620.3329-0.01820.5207-16.959157.144233.7308
130.09860.06760.02060.04550.01310.00720.0648-0.09630.0310.00120.01860.01160.0008-0.0662-0.03760.25770.02940.06330.33770.04470.3524-8.23847.373224.6439
140.0782-0.0715-0.0350.0710.0410.0243-0.04360.0894-0.08590.0382-0.03590.0248-0.0025-0.02340.04880.19430.04160.1020.3050.02260.23854.647458.118330.5423
150.0294-0.05160.04950.34850.00650.1385-0.0201-0.1609-0.0466-0.04680.01870.09-0.0401-0.07350.02260.22760.0330.06110.30270.00960.3442-12.252853.967922.5298
160.124-0.0351-0.15730.46550.40050.4778-0.1082-0.15510.27090.0228-0.10.1647-0.0007-0.11330.14530.39190.24770.10220.5720.03990.6627-26.335355.546835.3054
170.0003-0.00070.00040.00100.0014-0.0651-0.028-0.0234-0.0043-0.02110.01920.00870.0430.03570.19670.0437-0.05640.34010.07270.6912-41.241865.098830.0869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:108)
2X-RAY DIFFRACTION2(chain A and resid 109:235)
3X-RAY DIFFRACTION3(chain A and resid 236:301)
4X-RAY DIFFRACTION4(chain A and resid 302:323)
5X-RAY DIFFRACTION5(chain A and resid 324:466)
6X-RAY DIFFRACTION6(chain A and resid 467:539)
7X-RAY DIFFRACTION7(chain A and resid 540:682)
8X-RAY DIFFRACTION8(chain A and resid 683:766)
9X-RAY DIFFRACTION9(chain A and resid 767:863)
10X-RAY DIFFRACTION10(chain A and resid 864:902)
11X-RAY DIFFRACTION11(chain P and resid 102:107)
12X-RAY DIFFRACTION12(chain P and resid 108:111)
13X-RAY DIFFRACTION13(chain P and resid 112:115)
14X-RAY DIFFRACTION14(chain T and resid 1:4)
15X-RAY DIFFRACTION15(chain T and resid 5:9)
16X-RAY DIFFRACTION16(chain T and resid 10:14)
17X-RAY DIFFRACTION17(chain T and resid 15:18)

+
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