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- PDB-8xaq: The thermostable and acid-tolerant DNA-binding protein -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8xaq
TitleThe thermostable and acid-tolerant DNA-binding protein
ComponentsDNA/RNA-binding protein Alba
KeywordsDNA BINDING PROTEIN / Thermostable / Acid-tolerant DNA-binding protein
Function / homology
Function and homology information


chromosome condensation / chromosome / double-stranded 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/RNA-binding protein Alba
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChen, C.Y. / Huang, C.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U22A20551 China
CitationJournal: Heliyon / Year: 2024
Title: Dual dimeric interactions in the nucleic acid-binding protein Sac10b lead to multiple bridging of double-stranded DNA.
Authors: Tang, S. / Huang, C.H. / Ko, T.P. / Lin, K.F. / Chang, Y.C. / Lin, P.Y. / Sun, L. / Chen, C.Y.
History
DepositionDec 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA/RNA-binding protein Alba
B: DNA/RNA-binding protein Alba


Theoretical massNumber of molelcules
Total (without water)20,8862
Polymers20,8862
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-8 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.074, 38.895, 69.120
Angle α, β, γ (deg.)90.000, 131.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA/RNA-binding protein Alba


Mass: 10443.203 Da / Num. of mol.: 2 / Mutation: F59A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: albA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4J973
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 1000, 0.1M imidazole, pH 8.0, 0.2M Ca(OAc)2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 36860 / % possible obs: 98.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.54
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.41 / Num. unique obs: 36860

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DI4

7di4
PDB Unreleased entry


Resolution: 1.4→25.03 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1728 5.32 %
Rwork0.22 30729 -
obs0.222 32457 86.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.19 Å2 / Biso mean: 22.44 Å2 / Biso min: 9.52 Å2
Refinement stepCycle: final / Resolution: 1.4→25.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 0 195 1571
Biso mean---29.19 -
Num. residues----182
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 (%)
1.4-1.440.29811020.23941559166153
1.44-1.490.225790.23691789186860
1.49-1.540.2215940.2192026212069
1.54-1.60.24631470.23552292243978
1.6-1.670.28391280.23372585271388
1.67-1.760.25751360.23282888302497
1.76-1.870.2751760.23632881305799
1.87-2.020.24911650.23122924308999
2.02-2.220.26431630.20982970313399
2.22-2.540.25591700.22012924309499
2.54-3.20.25212210.222329093130100
3.2-25.030.24251470.20922982312997
Refinement TLS params.Method: refined / Origin x: 10.0814 Å / Origin y: 19.3958 Å / Origin z: 10.9892 Å
111213212223313233
T0.0731 Å20.0027 Å2-0.0026 Å2-0.0654 Å2-0.0029 Å2--0.0818 Å2
L1.0461 °2-0.0699 °2-0.3788 °2-1.4867 °20.1065 °2--1.152 °2
S-0.0054 Å °0.0972 Å °0.0332 Å °-0.0363 Å °0.0287 Å °0.0743 Å °0.0125 Å °-0.1143 Å °-0.0182 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA4 - 95
2X-RAY DIFFRACTION1ALLA101 - 194
3X-RAY DIFFRACTION1ALLB4 - 95
4X-RAY DIFFRACTION1ALLB101 - 201

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