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- PDB-1wto: Hyperthermophile chromosomal protein SAC7D double mutant V26F/M29... -

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Basic information

Entry
Database: PDB / ID: 1wto
TitleHyperthermophile chromosomal protein SAC7D double mutant V26F/M29F in complex with DNA GCGATCGC
Components
  • 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
  • DNA-binding proteins 7a/7b/7d
KeywordsDNA BINDING PROTEIN/DNA / COMPLEX CHROMATIN PROTEIN-DNA / MINOR-GROOVE DNA BINDING / ARCHEA / KINKED-DNA / INTERCALATION / Sac7d mutant / DNA BINDING 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: 1.5 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 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 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: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)12,5463
Polymers12,5463
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.900, 47.170, 60.260
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 / 7 KD HYPERTHERMOPHILE DNA-BINDING PROTEIN / 7 kDa DNA-binding proteins a/b/d / Sac7d


Mass: 7690.935 Da / Num. of mol.: 1 / Mutation: V26F/M29F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
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.: 191 / 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: 2.115 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 400, Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2Tris buffer11
3PEG 40012
4Tris buffer12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11501
21501
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL17B211.11634
SYNCHROTRONPhoton Factory BL-18B20.9194, 0.9200, 0.9184
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEAug 27, 2002
ADSC QUANTUM 42CCDDec 7, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.116341
20.91941
30.921
40.91841
ReflectionResolution: 1.5→40 Å / Num. all: 17486 / Num. obs: 16734 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 4.17 / Num. unique all: 1692 / % possible all: 94.2

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.5→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 795 -RANDOM
Rwork0.214 ---
all0.2145 17438 --
obs0.2145 16272 93.3 %-
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-6 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms532 322 0 191 1045
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.72
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.28 68 -
Rwork0.261 --
obs--81.8 %

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