[English] 日本語
Yorodumi
- PDB-8xap: Thermostable and acid-tolerant DNA-binding protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xap
TitleThermostable and acid-tolerant DNA-binding protein
ComponentsDNA binding protein alba-1
KeywordsDNA BINDING PROTEIN / Thermostable / Acid-tolerant DNA-binding protein
Function / homology
Function and homology information


chromosome condensation / chromosome / DNA binding / RNA binding / cytoplasm
Similarity search - Function
DNA/RNA-binding protein Alba / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily
Similarity search - Domain/homology
DNA binding protein alba-1
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChen, C.Y. / Huang, C.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U22A20551 China
CitationJournal: To Be Published
Title: Crystal structures of the thermostable and acid-tolerant DNA-binding proteins, Sac10b1, Sac10b2 and Sac10b1-F59A from Sulfolobus acidocaldarius
Authors: Chne, C.Y. / Huang, C.H.
History
DepositionDec 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA binding protein alba-1
B: DNA binding protein alba-1
C: DNA binding protein alba-1


Theoretical massNumber of molelcules
Total (without water)31,9363
Polymers31,9363
Non-polymers00
Water4,107228
1
A: DNA binding protein alba-1

C: DNA binding protein alba-1


Theoretical massNumber of molelcules
Total (without water)21,2912
Polymers21,2912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455x-1/2,y+1/2,z1
Buried area1260 Å2
ΔGint-8 kcal/mol
Surface area9460 Å2
MethodPISA
2
B: DNA binding protein alba-1

B: DNA binding protein alba-1


Theoretical massNumber of molelcules
Total (without water)21,2912
Polymers21,2912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1180 Å2
ΔGint-9 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.253, 68.922, 173.558
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-153-

HOH

21B-290-

HOH

31B-295-

HOH

-
Components

#1: Protein DNA binding protein alba-1


Mass: 10645.344 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: Saci_1321 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4J974
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate, pH 4.6, 2.0M sodium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 32123 / % possible obs: 99 % / Redundancy: 5.8 % / CC1/2: 0.965 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.026 / Rsym value: 0.053 / Net I/σ(I): 35.2
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.439 / Num. unique obs: 3197 / CC1/2: 0.857 / Rpim(I) all: 0.2 / Rsym value: 0.467

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→29.61 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 1651 5.15 %
Rwork0.207 30434 -
obs0.209 32085 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.75 Å2 / Biso mean: 41.3883 Å2 / Biso min: 17.38 Å2
Refinement stepCycle: final / Resolution: 1.7→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 0 234 2311
Biso mean---46.83 -
Num. residues----250
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.750.25681480.241625222670100
1.75-1.810.28321430.229524952638100
1.81-1.870.25251490.223525262675100
1.87-1.940.2711390.230525132652100
1.94-2.030.24911430.209125432686100
2.03-2.140.25931240.210825322656100
2.14-2.270.22841340.214625542688100
2.27-2.450.25761410.210125552696100
2.45-2.70.29011450.227925542699100
2.7-3.090.27211210.22625812702100
3.09-3.890.23631340.19182595272999
3.89-29.610.21491300.19132464259490
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)
15.5038-1.87691.85714.7159-0.81054.71110.08230.45620.2445-0.0919-0.1555-0.2999-0.16310.56160.06990.22810.0343-0.02590.31260.01860.24732.87525.583-23.608
22.1628-0.0712-0.1281.9074-1.21774.273-0.02170.03640.133-0.0825-0.0699-0.0297-0.23520.15450.07010.23470.0099-0.01120.12010.00370.21939.42510.809-2.213
33.6468-1.09960.50242.3887-2.09528.6166-0.09850.39080.1557-0.1546-0.02840.09870.0185-0.25960.09190.3028-0.0121-0.09470.3113-0.00350.31387.227-1.665-31.335
40.6101-0.57650.10960.59-0.34231.34410.05310.02130.037-0.0535-0.0792-0.0125-0.10070.05430.00050.3108-0.0317-0.02920.27-0.01240.33166.31710.183-13.023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:90 )A5 - 90
2X-RAY DIFFRACTION2( CHAIN B AND RESID 5:90 )B5 - 90
3X-RAY DIFFRACTION3( CHAIN C AND RESID 6:88 )C6 - 88
4X-RAY DIFFRACTION4( CHAIN A AND RESID 101:161 ) OR ( CHAIN B AND RESID 201:313 ) OR ( CHAIN C AND RESID 101:154 )A101 - 161
5X-RAY DIFFRACTION4( CHAIN A AND RESID 101:161 ) OR ( CHAIN B AND RESID 201:313 ) OR ( CHAIN C AND RESID 101:154 )B201 - 313
6X-RAY DIFFRACTION4( CHAIN A AND RESID 101:161 ) OR ( CHAIN B AND RESID 201:313 ) OR ( CHAIN C AND RESID 101:154 )C101 - 154

+
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