[English] 日本語
Yorodumi
- PDB-3syz: Crystal structure of the large fragment of DNA polymerase I from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3syz
TitleCrystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase
Components
  • (5'-D(*AP*AP*AP*(BMN)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
  • DNA polymerase I, thermostable
KeywordsTRANSFERASE/DNA / DNA polymerase / artificial base / TRANSFERASE-DNA complex
Function / homology
Function and homology information


nucleoside binding / 5'-3' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 ...Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / PIN-like domain superfamily / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier Techniques / Resolution: 1.952 Å
AuthorsBetz, K. / Diederichs, K. / Marx, A.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.
Authors: Betz, K. / Malyshev, D.A. / Lavergne, T. / Welte, W. / Diederichs, K. / Dwyer, T.J. / Ordoukhanian, P. / Romesberg, F.E. / Marx, A.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references
Revision 1.2Sep 12, 2012Group: Database references
Revision 1.3Sep 13, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: DNA polymerase I, thermostable
B: (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
C: (5'-D(*AP*AP*AP*(BMN)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,77121
Polymers69,5263
Non-polymers1,24618
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-30 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.529, 108.529, 90.524
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-850-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase I, thermostable / Taq polymerase 1


Mass: 60936.965 Da / Num. of mol.: 1 / Fragment: Klenow Fragment, UNP residues 293-832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: pol I, pol1, polA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P19821, DNA-directed DNA polymerase

-
DNA chain , 2 types, 2 molecules BC

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


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesizer
#3: DNA chain (5'-D(*AP*AP*AP*(BMN)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4971.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesizer

-
Non-polymers , 4 types, 342 molecules

#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 11% PEG 8000, 0.2M MgFormate, 0.1M Tris, 20mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0015 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0015 Å / Relative weight: 1
ReflectionResolution: 1.95→47 Å / Num. all: 45113 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Net I/σ(I): 11.23
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 2.21 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: Difference Fourier Techniques
Starting model: PDB ENTRY 4KTQ

4ktq


Resolution: 1.952→46.543 Å / SU ML: 0.47 / Isotropic thermal model: isotropic and tls / σ(F): 1.44 / Phase error: 18.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2013 4367 5.05 %
Rwork0.1602 --
obs0.1623 86484 99.7 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.198 Å2 / ksol: 0.412 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9774 Å2-0 Å2-0 Å2
2--0.9774 Å2-0 Å2
3----1.9548 Å2
Refinement stepCycle: LAST / Resolution: 1.952→46.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4266 571 80 324 5241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065142
X-RAY DIFFRACTIONf_angle_d1.0777068
X-RAY DIFFRACTIONf_dihedral_angle_d16.7762008
X-RAY DIFFRACTIONf_chiral_restr0.061772
X-RAY DIFFRACTIONf_plane_restr0.005822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9518-1.9740.27971440.25992529X-RAY DIFFRACTION91
1.974-1.99720.23941480.22922722X-RAY DIFFRACTION100
1.9972-2.02160.26861670.21652749X-RAY DIFFRACTION100
2.0216-2.04720.23421360.21472815X-RAY DIFFRACTION100
2.0472-2.07410.29581420.2092656X-RAY DIFFRACTION100
2.0741-2.10250.24151470.19612746X-RAY DIFFRACTION100
2.1025-2.13250.24991350.19422771X-RAY DIFFRACTION100
2.1325-2.16440.2271230.18152737X-RAY DIFFRACTION100
2.1644-2.19820.25641410.18562786X-RAY DIFFRACTION100
2.1982-2.23420.22621150.17412741X-RAY DIFFRACTION100
2.2342-2.27280.23861510.16682770X-RAY DIFFRACTION100
2.2728-2.31410.20561470.172736X-RAY DIFFRACTION100
2.3141-2.35860.22111260.17622774X-RAY DIFFRACTION100
2.3586-2.40670.27381170.17322727X-RAY DIFFRACTION100
2.4067-2.45910.25021350.16832768X-RAY DIFFRACTION100
2.4591-2.51630.23651650.16662763X-RAY DIFFRACTION100
2.5163-2.57920.23421390.16792744X-RAY DIFFRACTION100
2.5792-2.64890.25351630.16692726X-RAY DIFFRACTION100
2.6489-2.72690.23411550.16052696X-RAY DIFFRACTION100
2.7269-2.81490.22951420.16012786X-RAY DIFFRACTION100
2.8149-2.91550.21041550.14962684X-RAY DIFFRACTION100
2.9155-3.03220.1741460.15042779X-RAY DIFFRACTION100
3.0322-3.17010.15921310.1442760X-RAY DIFFRACTION100
3.1701-3.33720.17371650.14152704X-RAY DIFFRACTION100
3.3372-3.54620.16391490.13292772X-RAY DIFFRACTION100
3.5462-3.81990.17011680.13592729X-RAY DIFFRACTION100
3.8199-4.20410.16671770.13892699X-RAY DIFFRACTION100
4.2041-4.81190.16241310.12572759X-RAY DIFFRACTION100
4.8119-6.06040.22481460.17222758X-RAY DIFFRACTION100
6.0604-46.5560.18831610.18412731X-RAY DIFFRACTION100
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)
11.6084-0.0305-0.32792.4588-0.17361.0012-0.00110.0086-0.2196-0.1163-0.0336-0.27490.16910.12210.04020.1846-0.00340.0030.1783-0.00460.165239.8577-41.6799-18.3388
20.54860.58620.34520.97620.33291.2566-0.0144-0.08540.19270.0695-0.01040.1154-0.1605-0.03630.03330.1942-0.00080.02830.1898-0.0060.223231.194-12.7109-2.1252
35.42870.7694-2.19676.35210.76976.87410.3139-0.9881.51871.14580.11470.6407-1.6821-0.6189-0.39280.74530.12230.22170.7117-0.11540.83646.3466-12.3869-0.4881
42.00020.4306-0.3861.702-1.06732.47270.0108-0.07230.01610.03670.1280.2226-0.0856-0.2767-0.11110.1643-0.0074-0.00030.19250.00470.165418.2352-25.8501-14.4557
53.7271.1580.21152.5779-0.5521.41570.06070.2028-0.53760.5367-0.2643-0.0391-0.14120.62880.1220.25210.0388-0.00290.3-0.01150.25136.5971-22.9074.426
61.55771.4725-1.13153.85670.99392.5915-0.2905-0.02650.02140.14670.11630.11440.01170.01130.21130.19620.0151-0.01210.19710.00590.142333.437-22.90644.3367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 293:450)
2X-RAY DIFFRACTION2(chain A and resid 451:635)
3X-RAY DIFFRACTION3(chain A and resid 636:693)
4X-RAY DIFFRACTION4(chain A and resid 694:832)
5X-RAY DIFFRACTION5(chain B and resid 101:112)
6X-RAY DIFFRACTION6(chain C and resid 202:216)

+
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