[English] 日本語
Yorodumi
- PDB-4da2: The structure of Pyrococcus Furiosus SfsA in complex with Ca2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4da2
TitleThe structure of Pyrococcus Furiosus SfsA in complex with Ca2+
ComponentsSugar fermentation stimulation protein homolog
KeywordsDNA BINDING PROTEIN / OB fold / PD-(D/E)xK domain / nuclease
Function / homology
Function and homology information


OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #580 / Trna Endonuclease; Chain: A, domain 1 - #60 / Sugar fermentation stimulation protein / Sugar fermentation stimulation protein, C-terminal / SfsA, N-terminal OB domain / Sugar fermentation stimulation protein RE domain / SfsA N-terminal OB domain / Trna Endonuclease; Chain: A, domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #580 / Trna Endonuclease; Chain: A, domain 1 - #60 / Sugar fermentation stimulation protein / Sugar fermentation stimulation protein, C-terminal / SfsA, N-terminal OB domain / Sugar fermentation stimulation protein RE domain / SfsA N-terminal OB domain / Trna Endonuclease; Chain: A, domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sugar fermentation stimulation protein homolog
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsBaker, P.J. / Allen, F.L.
CitationJournal: To be Published
Title: The structure of SfsA and its DNA complex; A DNA/RNA nuclease with a novel domain combination
Authors: Allen, F.L. / Akerboom, J. / Bliss, S.J. / Blombach, F. / Sedelnikova, S.E. / van der Oost, J. / Baker, P.J.
History
DepositionJan 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sugar fermentation stimulation protein homolog
B: Sugar fermentation stimulation protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6196
Polymers52,4582
Non-polymers1604
Water2,954164
1
A: Sugar fermentation stimulation protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3093
Polymers26,2291
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sugar fermentation stimulation protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3093
Polymers26,2291
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.017, 46.017, 194.575
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein Sugar fermentation stimulation protein homolog


Mass: 26229.098 Da / Num. of mol.: 2 / Mutation: L120I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1198, sfsA / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U1K8
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 4.6
Details: 30% (w/v) PEG 3350, 0.2 M calcium acetate, 0.01 M sodium acetate and 0.22 M potassium chloride pH 4.6, vapor diffusion, temperature 290K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.975564
SYNCHROTRONESRF ID2920.9793, 0.9795, 0.9755
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDDec 16, 2008
DECTRIS PILATUS 6M2PIXELMay 11, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond Beamline I03SINGLE WAVELENGTHMx-ray1
2liquid nitrogen cooled channel-cut silicon monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9755641
20.97931
30.97951
40.97551
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.624
11K, H, -L20.376
ReflectionResolution: 1.8→64.8 Å / Num. all: 42809 / Num. obs: 42809 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.45 / % possible all: 100

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
GDAdata collection
RefinementMethod to determine structure: MAD / Resolution: 1.8→196.19 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.422 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1716 2120 5 %RANDOM
Rwork0.1361 ---
all0.14 42809 --
obs0.1379 42741 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 449.72 Å2 / Biso mean: 25.0569 Å2 / Biso min: 5.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0 Å20 Å2
2---0.84 Å2-0 Å2
3---1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.8→196.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3676 0 4 164 3844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223736
X-RAY DIFFRACTIONr_angle_refined_deg1.3742.015004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.63622.179156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94815752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0631542
X-RAY DIFFRACTIONr_chiral_restr0.0940.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212724
X-RAY DIFFRACTIONr_mcbond_it8.6122288
X-RAY DIFFRACTIONr_mcangle_it8.95433686
X-RAY DIFFRACTIONr_scbond_it34.05821448
X-RAY DIFFRACTIONr_scangle_it27.4631318
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 135 -
Rwork0.181 3053 -
all-3188 -
obs--98.09 %

+
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