[English] 日本語
Yorodumi
- PDB-3ft7: Crystal structure of an extremely stable dimeric protein from sul... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ft7
TitleCrystal structure of an extremely stable dimeric protein from sulfolobus islandicus
ComponentsUncharacterized protein ORF56
KeywordsDNA BINDING PROTEIN / PLASMID COPY CONTROL PROTEIN / RIBBON HELIX HELIX PROTEIN
Function / homologyMet repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / regulation of DNA-templated transcription / Orthogonal Bundle / Mainly Alpha / CopG domain protein DNA-binding domain protein
Function and homology information
Biological speciesSulfolobus islandicus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsNeumann, P. / Loew, C. / Weininger, U. / Stubbs, M.T.
CitationJournal: Biochemistry / Year: 2009
Title: Structure-Based Stability Analysis of an Extremely Stable Dimeric DNA Binding Protein from Sulfolobus islandicus
Authors: Weininger, U. / Zeeb, M. / Neumann, P. / Low, C. / Stubbs, M.T. / Lipps, G. / Balbach, J.
History
DepositionJan 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Uncharacterized protein ORF56
B: Uncharacterized protein ORF56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1653
Polymers13,0732
Non-polymers921
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-27 kcal/mol
Surface area5540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.030, 33.030, 85.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Uncharacterized protein ORF56


Mass: 6536.647 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus (archaea) / Gene: PLASMID PRN1 / Plasmid: PET28C? / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q54323
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.7877 Å3/Da / Density % sol: 31.1971 % / Mosaicity: 0.75 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16-22% PEG 4000, 100mM HEPES pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 7, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.481
ReflectionResolution: 2→85.749 Å / Num. obs: 6218 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 26.651 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 6.307
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.114.20.6231.238469110.62399.7
2.11-2.244.20.4251.935718510.42599.9
2.24-2.394.20.2982.634288090.29899.9
2.39-2.584.20.2123.631817530.21299.8
2.58-2.834.20.1425.529536960.14299.8
2.83-3.164.30.0839.126626250.08399.8
3.16-3.654.30.06110.823845600.06199.6
3.65-4.474.30.04512.819194460.04599.1
4.47-6.324.30.0471115803670.04798.5
6.32-33.034.20.03411.98402000.03498.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345225data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MYK, 1PAR

1myk

1par


Resolution: 2→33.03 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: Isotropic, TLS refinement / Cross valid method: THROUGHOUT / σ(F): 1.47 / σ(I): 0 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1077 9.13 %RANDOM
Rwork0.171 ---
obs0.177 5849 96.22 %-
all-11792 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 89.474 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 132.3 Å2 / Biso mean: 49.037 Å2 / Biso min: 9.88 Å2
Baniso -1Baniso -2Baniso -3
1-5.628 Å20 Å2-0 Å2
2--5.628 Å20 Å2
3----15.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.278 Å0.234 Å
Luzzati d res low-6 Å
Luzzati sigma a0.267 Å0.256 Å
Refinement stepCycle: LAST / Resolution: 2→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms744 0 6 41 791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016761
X-RAY DIFFRACTIONf_angle_d1.9331024
X-RAY DIFFRACTIONf_chiral_restr0.103116
X-RAY DIFFRACTIONf_plane_restr0.008127
X-RAY DIFFRACTIONf_dihedral_angle_d21.949285
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.1250.3441630.28218031966
2.125-2.2890.2961720.24617571929
2.289-2.520.3331440.24118361980
2.52-2.8840.2921740.19717661940
2.884-3.6330.2452010.14717951996
3.633-33.0350.1721770.12318041981
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)
11.5303-0.2599-0.19680.60580.14481.2517-0.39470.0305-0.12480.07790.09220.23840.0651-0.00380.31640.2097-0.02430.03990.03050.00010.09825.6027-2.8007-3.8011
20.7812-0.18870.00440.2758-1.05860.5308-0.30870.00830.05550.1310.1638-0.06370.2135-0.19040.07120.31270.0488-0.03240.0693-0.00970.04375.71672.34283.7106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

+
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