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- PDB-1xyi: Hyperthermophile chromosomal protein Sac7d double mutant Val26Ala... -

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Basic information

Entry
Database: PDB / ID: 1xyi
TitleHyperthermophile chromosomal protein Sac7d double mutant Val26Ala/Met29Ala in complex with DNA GCGATCGC
Components
  • 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
  • DNA-binding proteins 7a/7b/7d
KeywordsSTRUCTURAL PROTEIN/DNA / PROTEIN-DNA COMPLEX / Oligonucleotide binding fold / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


RNA endonuclease activity / DNA binding / cytoplasm
Similarity search - Function
DNA-binding 7kDa protein / 7kD DNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA-binding protein 7d
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsChen, C.-Y. / Ko, T.-P. / Lin, T.-W. / Chou, C.-C. / Chen, C.-J. / Wang, A.H.-J.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d
Authors: Chen, C.-Y. / Ko, T.-P. / Lin, T.-W. / Chou, C.-C. / Chen, C.-J. / Wang, A.H.-J.
History
DepositionNov 10, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Advisory / Database references
Category: database_2 / pdbx_validate_close_contact / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
C: 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
A: DNA-binding proteins 7a/7b/7d


Theoretical massNumber of molelcules
Total (without water)12,3943
Polymers12,3943
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.780, 47.270, 52.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'


Mass: 2427.605 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA-binding proteins 7a/7b/7d / chromosomal protein Sac7d


Mass: 7538.743 Da / Num. of mol.: 1 / Mutation: V26A, M29A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: sac7d / Plasmid: PET3b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P13123
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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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: 1.896 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Tris, PEG400, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris11
2PEG40011
3Tris12
4PEG40012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.0717 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 28, 2002 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0717 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 17294 / Num. obs: 17190 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 33.7
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 4.88 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1712 / % possible all: 99.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.45→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 808 -RANDOM
Rwork0.214 ---
all0.216 17294 --
obs0.216 16568 95.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms520 322 0 207 1049
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.9
LS refinement shellResolution: 1.45→1.5 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.329 88 -
Rwork0.301 --
obs--85.6 %

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