[English] 日本語
Yorodumi
- PDB-4flt: Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in ed... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4flt
TitlePyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode
Components
  • DNA polymerase 1
  • Primer strand
  • Template strand
KeywordsTRANSFERASE/DNA / DNA polymerase / DNA binding / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
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 / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. ...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 / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Helix Hairpins / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase 1
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGouge, J. / Delarue, M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase.
Authors: Gouge, J. / Ralec, C. / Henneke, G. / Delarue, M.
History
DepositionJun 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Database references / Source and taxonomy
Category: pdbx_entity_src_syn / reflns / struct_ref_seq_dif
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
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_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.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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase 1
P: Primer strand
T: Template strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5777
Polymers99,2413
Non-polymers3364
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-31 kcal/mol
Surface area35290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.930, 114.400, 128.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase 1 / Pab polymerase


Mass: 91809.938 Da / Num. of mol.: 1 / Mutation: D215A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5 / Orsay / Gene: polI, pol, PYRAB17200, PAB1128 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CL77, DNA-directed DNA polymerase

-
DNA chain , 2 types, 2 molecules PT

#2: DNA chain Primer strand


Mass: 3399.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others)
#3: DNA chain Template strand


Mass: 4031.634 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 317 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7-12% PEG 20000, 100 mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2011
RadiationMonochromator: ID14-1 Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.9→47 Å / Num. obs: 22297 / % possible obs: 97.2 % / Redundancy: 4 % / Biso Wilson estimate: 55.36 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 11.2
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3248 / Rsym value: 0.25 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FLW

4flw


Resolution: 2.9→44.02 Å / Cor.coef. Fo:Fc: 0.9241 / Cor.coef. Fo:Fc free: 0.8904 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 1146 5.15 %RANDOM
Rwork0.1639 ---
obs0.1661 22265 96 %-
all-21903 --
Displacement parametersBiso mean: 30.24 Å2
Baniso -1Baniso -2Baniso -3
1-5.9433 Å20 Å20 Å2
2--2.029 Å20 Å2
3----7.9723 Å2
Refine analyzeLuzzati coordinate error obs: 0.293 Å
Refinement stepCycle: LAST / Resolution: 2.9→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6107 476 20 313 6916
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016806HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.119293HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3225SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes142HARMONIC2
X-RAY DIFFRACTIONt_gen_planes918HARMONIC5
X-RAY DIFFRACTIONt_it6806HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion3.15
X-RAY DIFFRACTIONt_chiral_improper_torsion871SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7639SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.04 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2594 155 5.23 %
Rwork0.1927 2808 -
all0.1961 2963 -
obs--96 %
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)
13.6726-1.15851.22151.7783-1.2211.9969-0.0564-0.4433-0.45140.14460.09490.27020.1441-0.2199-0.0386-0.11410.01220.0714-0.110.0127-0.018311.5041-51.771-9.3909
21.468-0.5268-0.22541.33210.49191.30480.0284-0.02860.0267-0.112-0.01470.1186-0.18780.0038-0.0137-0.07410.0118-0.0023-0.05410.0037-0.0669-1.3714-22.2125-24.2919
32.44660.5262-1.41920.5827-2.24230.54440.0398-0.3331-0.02870.1146-0.04230.1425-0.26010.13790.00260.0261-0.0490.034-0.0999-0.0589-0.064427.9528-38.1019-15.6634
40.784-0.13190.14171.7309-0.04210.57050.00080.06750.0149-0.2028-0.0317-0.16060.04240.00540.0309-0.07830.03620.0146-0.02-0.0166-0.056434.3863-34.2133-32.7659
51.78930.261-0.53530.6785-0.65931.54360.1227-0.23220.11770.1165-0.0647-0.0048-0.2442-0.0447-0.058-0.0386-0.03980.0287-0.0859-0.0181-0.070419.2315-2.6077-13.8894
601.85130.01150.28960.13313.03420.0019-0.1340.02420.1761-0.0306-0.145-0.04120.17530.0287-0.04970.0270.0143-0.0056-0.02670.044135.3414-0.3082-19.9753
70.39790.36050.35510-0.38282.4889-0.028-0.1457-0.2667-0.09080.0496-0.21350.16720.2333-0.0216-0.0741-0.065-0.04020.0278-0.00570.05823.6665-16.5026-2.3413
80-0.4726-1.75541.13681.32110.5192-0.02270.01890.07180.21220.08020.08-0.046-0.0303-0.0575-0.0308-0.01370.0686-0.01630.0220.02347.8116-15.3154-18.6028
900.18982.72880.331-0.09320.975-0.0039-0.03180.15320.01990.0088-0.03620.00680.0489-0.00490.1163-0.0241-0.05220.0207-0.01880.030813.4255-36.9607-10.2673
101.5243-2.7268-0.11863.2148-0.78690.4237-0.01960.1079-0.0935-0.118-0.0649-0.2215-0.02550.15360.0845-0.2193-0.0854-0.0773-0.0366-0.03790.045924.4003-15.2173-6.8776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|-1 - 134}A-1 - 134
2X-RAY DIFFRACTION2{A|135 - 347}A135 - 347
3X-RAY DIFFRACTION3{A|348 - 394}A348 - 394
4X-RAY DIFFRACTION4{A|395 - 583}A395 - 583
5X-RAY DIFFRACTION5{A|584 - 741}A584 - 741
6X-RAY DIFFRACTION6{A|742 - 757}A742 - 757
7X-RAY DIFFRACTION7{P|1 - 7}P1 - 7
8X-RAY DIFFRACTION8{P|8 - 11}P8 - 11
9X-RAY DIFFRACTION9{T|1 - 5}T1 - 5
10X-RAY DIFFRACTION10{T|6 - 13}T6 - 13

+
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