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- PDB-1wtp: Hyperthermophile chromosomal protein SAC7D single mutant M29F in ... -

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Basic information

Entry
Database: PDB / ID: 1wtp
TitleHyperthermophile chromosomal protein SAC7D single mutant M29F in complex with DNA GCGA(UBr)CGC
Components
  • 5'-D(*GP*CP*GP*AP*(BRU)P*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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,2566
Polymers25,2566
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.217, 47.889, 52.494
Angle α, β, γ (deg.)90.00, 102.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 2492.475 Da / Num. of mol.: 4 / 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: 7642.892 Da / Num. of mol.: 2 / Mutation: 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 / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.89 Å3/Da / Density % sol: 35 %
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

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 16, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 15060 / Num. obs: 14849 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 26.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 4 / Num. unique all: 1494 / % possible all: 93.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AZP

1azp


Resolution: 1.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2872 1434 -RANDOM
Rwork0.2216 ---
all0.228 14754 --
obs0.228 14194 96.2 %-
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 644 0 156 1827
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.66
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.044
RfactorNum. reflection% reflection
Rfree0.3703 118 -
Rwork0.3268 --
obs--84.7 %

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