[English] 日本語
Yorodumi
- PDB-1ksx: Crystal Structures of Two Intermediates in the Assembly of the Pa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ksx
TitleCrystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex
Components
  • E1 Recognition Sequence
  • REPLICATION PROTEIN E1
KeywordsREPLICATION/DNA / PAPILLOMAVIRUS / DNA-BINDING DOMAIN / REPLICATION / INITIATOR PROTEIN / HELICASE / REPLICATION-DNA COMPLEX
Function / homology
Function and homology information


DNA 3'-5' helicase / DNA helicase activity / DNA replication / host cell nucleus / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Replication Protein E1; Chain: A, - #10 / DNA helicase E1, C-terminal, Papillomavirus / DNA helicase E1, N-terminal, Papillomavirus / Replication protein E1, papillomavirus / DNA helicase E1, DNA-binding domain, papillomavirus / DNA helicase E1, DNA-binding domain superfamily, papillomavirus / Papillomavirus helicase / E1 Protein, N terminal domain / Papillomavirus E1, DNA-binding domain / Replication Protein E1; Chain: A, ...Replication Protein E1; Chain: A, - #10 / DNA helicase E1, C-terminal, Papillomavirus / DNA helicase E1, N-terminal, Papillomavirus / Replication protein E1, papillomavirus / DNA helicase E1, DNA-binding domain, papillomavirus / DNA helicase E1, DNA-binding domain superfamily, papillomavirus / Papillomavirus helicase / E1 Protein, N terminal domain / Papillomavirus E1, DNA-binding domain / Replication Protein E1; Chain: A, / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Replication protein E1
Similarity search - Component
Biological speciesBovine papillomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsEnemark, E.J. / Stenlund, A. / Joshua-Tor, L.
CitationJournal: EMBO J. / Year: 2002
Title: Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex.
Authors: Enemark, E.J. / Stenlund, A. / Joshua-Tor, L.
History
DepositionJan 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: E1 Recognition Sequence
G: E1 Recognition Sequence
K: E1 Recognition Sequence
O: E1 Recognition Sequence
A: REPLICATION PROTEIN E1
B: REPLICATION PROTEIN E1
E: REPLICATION PROTEIN E1
F: REPLICATION PROTEIN E1
I: REPLICATION PROTEIN E1
J: REPLICATION PROTEIN E1
M: REPLICATION PROTEIN E1
N: REPLICATION PROTEIN E1


Theoretical massNumber of molelcules
Total (without water)160,79912
Polymers160,79912
Non-polymers00
Water36020
1
C: E1 Recognition Sequence
G: E1 Recognition Sequence
A: REPLICATION PROTEIN E1
B: REPLICATION PROTEIN E1
E: REPLICATION PROTEIN E1
F: REPLICATION PROTEIN E1


Theoretical massNumber of molelcules
Total (without water)80,4006
Polymers80,4006
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: E1 Recognition Sequence
O: E1 Recognition Sequence
I: REPLICATION PROTEIN E1
J: REPLICATION PROTEIN E1
M: REPLICATION PROTEIN E1
N: REPLICATION PROTEIN E1


Theoretical massNumber of molelcules
Total (without water)80,4006
Polymers80,4006
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.246, 103.650, 124.996
Angle α, β, γ (deg.)90.00, 99.53, 90.00
Int Tables number4
Space group name H-MP1211
DetailsE1 multimerization occurs upon binding to the adjacent sites of the target DNA sequence.

-
Components

#1: DNA chain
E1 Recognition Sequence


Mass: 6444.222 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
REPLICATION PROTEIN E1


Mass: 16877.770 Da / Num. of mol.: 8 / Fragment: DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine papillomavirus / Plasmid: PET11CGST / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03116
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.33 Å3/Da / Density % sol: 63.05 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ca(CF3COO)2, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ca(CF3COO)211
2DTT11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mM1reservoirMgSO4
22.5 mMspermine tetrahydrochloride1reservoir
35 %ethylene glycol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 4, 2000 / Details: mirrors
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 35201 / Num. obs: 35038 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.195 / Net I/σ(I): 9.14
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3474 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 125960
Reflection shell
*PLUS
% possible obs: 99.3 % / Num. unique obs: 3474 / Num. measured obs: 12242

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F08

1f08


Resolution: 3.2→42.62 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 130431.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT IS LESS THAN SPECIFIED IN REMARK 3. THE VALUES LISTED IN REMARK 3 ARE 4-FOLD GREATER (REFLECTING THE 4-FOLD STRICT NCS). 2328 PROTEIN ...Details: THE NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT IS LESS THAN SPECIFIED IN REMARK 3. THE VALUES LISTED IN REMARK 3 ARE 4-FOLD GREATER (REFLECTING THE 4-FOLD STRICT NCS). 2328 PROTEIN ATOMS, 428 NUCLEIC ACID ATOMS, AND 5 SOLVENT ATOMS WERE USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1612 5.1 %RANDOM
Rwork0.263 ---
all-35201 --
obs-31865 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.0378 Å2 / ksol: 0.240909 e/Å3
Displacement parametersBiso mean: 59.5 Å2
Baniso -1Baniso -2Baniso -3
1-31.6 Å20 Å212.57 Å2
2---16.2 Å20 Å2
3----15.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a1 Å0.72 Å
Refinement stepCycle: LAST / Resolution: 3.2→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9312 1712 0 20 11044
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it10.221.5
X-RAY DIFFRACTIONc_mcangle_it15.212
X-RAY DIFFRACTIONc_scbond_it17.42
X-RAY DIFFRACTIONc_scangle_it24.342.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.429 237 5.1 %
Rwork0.382 4449 -
obs--80.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 50 Å / Rfactor obs: 0.2634 / Rfactor Rfree: 0.2844
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

+
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