[English] 日本語
Yorodumi
- PDB-3pr4: Dpo4 Y12A mutant incorporating dADP opposite template dT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pr4
TitleDpo4 Y12A mutant incorporating dADP opposite template dT
Components
  • DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*C)-3')
  • DNA (5'-D(*TP*TP*CP*AP*TP*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / DNA polymerase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol
Similarity search - Function
DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily ...DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKirouac, K.N. / Suo, Z. / Ling, H.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural mechanism of ribonucleotide discrimination by a Y-family DNA polymerase.
Authors: Kirouac, K.N. / Suo, Z. / Ling, H.
History
DepositionNov 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_seq_id / _struct_conn.ptnr2_label_asym_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 IV
P: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*C)-3')
T: DNA (5'-D(*TP*TP*CP*AP*TP*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0157
Polymers48,3883
Non-polymers6274
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-75 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.347, 102.004, 52.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase IV / / Pol IV


Mass: 38927.426 Da / Num. of mol.: 1 / Mutation: Y12A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: dbh, dpo4, SSO2448 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W02, DNA-directed DNA polymerase

-
DNA chain , 2 types, 2 molecules PT

#2: DNA chain DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*C)-3')


Mass: 4081.659 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*TP*CP*AP*TP*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')


Mass: 5378.478 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Non-polymers , 3 types, 88 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG 3350, 0.15M CaAc2, 0.1M Hepes pH 7.0, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 4, 2007
RadiationMonochromator: GRADED MULTILAYER (OSMIC) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. all: 15456 / Num. obs: 15419 / % possible obs: 99.24 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.65→2.79 Å / % possible all: 95

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JX4

1jx4


Resolution: 2.65→26.113 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 25.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 793 5.14 %RANDOM
Rwork0.1972 ---
all0.2028 15456 --
obs0.2 15419 99.24 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.207 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9275 Å20 Å20 Å2
2--1.1328 Å20 Å2
3---0.7947 Å2
Refinement stepCycle: LAST / Resolution: 2.65→26.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2655 570 29 84 3338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093359
X-RAY DIFFRACTIONf_angle_d1.2914656
X-RAY DIFFRACTIONf_dihedral_angle_d20.421306
X-RAY DIFFRACTIONf_chiral_restr0.067541
X-RAY DIFFRACTIONf_plane_restr0.005489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.81590.41631460.33522373X-RAY DIFFRACTION99
2.8159-3.0330.35311290.28752392X-RAY DIFFRACTION99
3.033-3.33770.30091150.22252449X-RAY DIFFRACTION100
3.3377-3.81930.26831310.1962440X-RAY DIFFRACTION100
3.8193-4.80710.20561260.15382461X-RAY DIFFRACTION100
4.8071-26.11430.21331460.17532511X-RAY DIFFRACTION97
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)
10.5361-0.68070.69151.1616-0.00040.8555-0.0176-0.1602-0.1762-0.03860.13720.0389-0.03950.1811-0.05410.2880.0263-0.01150.31590.0220.210330.29295.398819.797
22.0201-1.054-0.16041.76360.01440.416-0.283-0.52150.06340.01850.33350.14050.0535-0.0071-0.04070.20620.01310.00960.3272-0.04550.219812.762919.523417.7412
30.70840.5820.40831.4581-0.18790.5613-0.0225-0.26830.0956-0.4806-0.1214-0.0323-0.1402-0.57630.10540.39240.014-0.1060.4136-0.07270.374711.617828.949410.4394
42.0097-0.7209-0.19560.78780.26111.27750.11140.07790.2153-0.0494-0.1379-0.11160.38810.15630.01160.36620.09810.0390.32580.02160.287240.637516.3305-3.0914
50.4435-0.0716-0.34820.2238-0.08130.53570.2334-0.03970.2848-0.3250.22980.52780.26020.1355-0.28070.4609-0.0521-0.08720.32770.02710.584128.100130.2915-0.0767
60.850.6621-0.73181.29420.35730.3052-0.0503-0.19850.39220.09530.0360.3970.15460.4484-0.01480.39680.0856-0.04390.36970.00980.427331.072627.29911.1114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:91)
2X-RAY DIFFRACTION2(chain A and resid 92:219)
3X-RAY DIFFRACTION3(chain A and resid 220:239)
4X-RAY DIFFRACTION4(chain A and resid 240:341)
5X-RAY DIFFRACTION5(chain P and resid 1:13)
6X-RAY DIFFRACTION6(chain T and resid 2:17)

+
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