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

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Basic information

Entry
Database: PDB / ID: 8xao
TitleThe thermostable and acid-tolerant DNA-binding protein
ComponentsDNA/RNA-binding protein Alba
KeywordsDNA BINDING PROTEIN / Thermostable / Acid-tolerant DNA-binding proteins
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: 2.05 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2347
Polymers21,0392
Non-polymers1955
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-9 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.892, 81.892, 139.371
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-209-

HOH

21B-258-

HOH

31B-275-

HOH

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Components

#1: Protein DNA/RNA-binding protein Alba


Mass: 10519.300 Da / Num. of mol.: 2
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: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate pH 5.5, 0.2M KBr, 25% PEG 2000 MME

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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: 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: 2.05→30 Å / Num. obs: 17976 / % possible obs: 99.9 % / Redundancy: 9.3 % / CC1/2: 0.983 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.017 / Rsym value: 0.034 / Net I/σ(I): 39.8
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.575 / Num. unique obs: 1734 / CC1/2: 0.914 / Rpim(I) all: 0.2 / Rsym value: 0.426

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→28.19 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 841 5.16 %
Rwork0.2019 15450 -
obs0.2035 16291 90.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.94 Å2 / Biso mean: 30.179 Å2 / Biso min: 12.02 Å2
Refinement stepCycle: final / Resolution: 2.05→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 5 151 1489
Biso mean--31.79 36.74 -
Num. residues----173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.180.2473900.20261460155054
2.18-2.350.24561380.21432490262890
2.35-2.580.23111420.211228002942100
2.58-2.960.27831650.215828032968100
2.96-3.720.20661400.189528753015100
3.73-28.190.22171660.198930223188100
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)
15.94681.010.86023.0407-0.04534.60520.0726-0.59030.06190.1993-0.1061-0.0914-0.04990.16190.01990.1432-0.0170.00730.2065-0.03130.107915.384-34.7299.415
26.16570.2156-0.89981.71020.07253.3257-0.1102-0.1291-0.32730.04080.12580.1503-0.0423-0.19320.00810.14070.0189-0.0290.14540.00580.14052.225-42.263-3.408
33.39183.76780.69014.70760.59930.17580.03860.48080.45790.29780.0470.16480.1496-0.2884-0.1160.1774-0.009-0.05950.27680.08830.11568.678-36.122-8.303
41.6389-0.0280.07921.2704-0.07721.28280.008-0.0470.12360.03150.033-0.0354-0.206-0.0054-0.0420.17540.0174-0.01990.1582-0.00210.16879.5-36.3660.657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:96 )A9 - 96
2X-RAY DIFFRACTION2( CHAIN B AND RESID 5:96 )B5 - 96
3X-RAY DIFFRACTION3( CHAIN A AND RESID 101:101 ) OR ( CHAIN B AND RESID 101:104 )A101
4X-RAY DIFFRACTION3( CHAIN A AND RESID 101:101 ) OR ( CHAIN B AND RESID 101:104 )B101 - 104
5X-RAY DIFFRACTION4( CHAIN A AND RESID 201:263 ) OR ( CHAIN B AND RESID 201:283 )A201 - 263
6X-RAY DIFFRACTION4( CHAIN A AND RESID 201:263 ) OR ( CHAIN B AND RESID 201:283 )B201 - 283

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