[English] 日本語
Yorodumi
- PDB-4psn: Crystal structure of apeThermo-DBP-RP2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4psn
TitleCrystal structure of apeThermo-DBP-RP2
ComponentsssDNA binding protein
KeywordsDNA BINDING PROTEIN / ssDNA binding protein
Function / homology: / Thermo-DBP-RP2 C-terminal domain / ThermoDBP-related, archaea / ThermoDBP-related, archaea / IMIDAZOLE / Thermo-DBP-RP2-like C-terminal domain-containing protein
Function and homology information
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsGahlei, H. / von Moeller, H. / Eppers, D. / Loll, B. / Wahl, M.C.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein.
Authors: Ghalei, H. / Moeller, H.v. / Eppers, D. / Sohmen, D. / Wilson, D.N. / Loll, B. / Wahl, M.C.
History
DepositionMar 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: ssDNA binding protein
B: ssDNA binding protein
C: ssDNA binding protein
D: ssDNA binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,67112
Polymers107,0724
Non-polymers5998
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19690 Å2
ΔGint-25 kcal/mol
Surface area39140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.240, 108.640, 154.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
ssDNA binding protein


Mass: 26768.100 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea)
Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
Gene: APE_1866.1 / Plasmid: pET-M11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9YAS7
#2: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M imidazole, pH 8.0, 0.4 M NaH2PO4, 1.6 M K2HPO4, 0.2 M NaCl and 0.25 M glycine, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 7, 2010
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 125145 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 28.8 Å2
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 5.9 % / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
HKL2Mapmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→32.727 Å / SU ML: 0.25 / Phase error: 20.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 3207 5.05 %RANDOM
Rwork0.1793 ---
obs0.1811 63466 96.71 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.614 Å2 / ksol: 0.419 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6062 Å20 Å2-0 Å2
2--5.1365 Å20 Å2
3----3.5303 Å2
Refinement stepCycle: LAST / Resolution: 2.05→32.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6995 0 42 283 7320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087200
X-RAY DIFFRACTIONf_angle_d1.0829741
X-RAY DIFFRACTIONf_dihedral_angle_d14.9072765
X-RAY DIFFRACTIONf_chiral_restr0.0721161
X-RAY DIFFRACTIONf_plane_restr0.0041272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.08060.29841360.24182445X-RAY DIFFRACTION93
2.0806-2.11310.2651530.19022456X-RAY DIFFRACTION92
2.1131-2.14770.24021230.17712478X-RAY DIFFRACTION93
2.1477-2.18480.21911520.18192531X-RAY DIFFRACTION95
2.1848-2.22450.241310.18632507X-RAY DIFFRACTION93
2.2245-2.26730.26971160.21442393X-RAY DIFFRACTION89
2.2673-2.31350.22071260.17862521X-RAY DIFFRACTION94
2.3135-2.36380.26331370.17812559X-RAY DIFFRACTION96
2.3638-2.41880.24851230.19632601X-RAY DIFFRACTION97
2.4188-2.47930.26691500.1892589X-RAY DIFFRACTION97
2.4793-2.54630.25451450.1912601X-RAY DIFFRACTION97
2.5463-2.62120.25291330.18242615X-RAY DIFFRACTION97
2.6212-2.70570.21521320.1852639X-RAY DIFFRACTION97
2.7057-2.80240.23531520.19052639X-RAY DIFFRACTION98
2.8024-2.91450.22451530.18462687X-RAY DIFFRACTION99
2.9145-3.04710.23241540.18152656X-RAY DIFFRACTION99
3.0471-3.20760.22341330.17172715X-RAY DIFFRACTION99
3.2076-3.40840.17211570.16312683X-RAY DIFFRACTION100
3.4084-3.67120.19041350.16512709X-RAY DIFFRACTION100
3.6712-4.04010.19751260.1642759X-RAY DIFFRACTION100
4.0401-4.62330.17991380.15332772X-RAY DIFFRACTION100
4.6233-5.81950.19731370.17882792X-RAY DIFFRACTION100
5.8195-32.73130.21251650.20482912X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.3485 Å / Origin y: -15.9074 Å / Origin z: 38.1118 Å
111213212223313233
T0.0743 Å2-0.0043 Å2-0.0019 Å2-0.0854 Å2-0.0051 Å2--0.0809 Å2
L0.1888 °20.0002 °2-0.2771 °2-0.1262 °20.0767 °2--0.4232 °2
S0.0106 Å °0.013 Å °-0.0004 Å °0.0149 Å °0.0025 Å °0.0045 Å °0.0217 Å °-0.0359 Å °-0.0068 Å °
Refinement TLS groupSelection details: all

+
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