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- PDB-8xap: Thermostable and acid-tolerant DNA-binding protein -

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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: 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 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

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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

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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: 2.26 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

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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: 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

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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: 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

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