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- PDB-1ca5: INTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/... -

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Basic information

Entry
Database: PDB / ID: 1ca5
TitleINTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/SAC7D BOUND TO DNA
Components
  • 5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3'
  • CHROMOSOMAL PROTEIN SAC7DChromosome
KeywordsSTRUCTURAL PROTEIN/DNA / HYPERTHERMOPHILE / CHROMOSOMAL PROTEIN / SSO7D / SAC7D / DNA BINDING / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSu, S. / Gao, Y.-G. / Robinson, H. / Shriver, J.W. / Wang, A.H.-J.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs
Authors: Su, S. / Gao, Y.-G. / Robinson, H. / Liaw, Y.C. / Edmondson, S.P. / Shriver, J.W. / Wang, A.H.-J.
#1: Journal: Nature / Year: 1998
Title: The hyperthermophile chromosomal protein Sac7d sharply kinks DNA.
Authors: Robinson, H. / Gao, Y.G. / McCrary, B.S. / Edmondson, S.P. / Shriver, J.W. / Wang, A.H.
#2: Journal: Nat.Struct.Biol. / Year: 1998
Title: The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA.
Authors: Gao, Y.G. / Su, S.Y. / Robinson, H. / Padmanabhan, S. / Lim, L. / McCrary, B.S. / Edmondson, S.P. / Shriver, J.W. / Wang, A.H.
History
DepositionFeb 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Advisory
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Nov 6, 2019Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / pdbx_entity_src_syn
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.6Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3'
C: 5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3'
A: CHROMOSOMAL PROTEIN SAC7D


Theoretical massNumber of molelcules
Total (without water)12,4803
Polymers12,4803
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.780, 76.760, 35.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein CHROMOSOMAL PROTEIN SAC7D / Chromosome


Mass: 7626.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sulfolobus acidocaldarius (acidophilic) / References: UniProt: P13123
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.7 Å3/Da / Density % sol: 53 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.3 mMSac7d1drop
21.3 mMDNA duplex1drop
32.5 mMTris-HCl1drop
42 %PEG4001drop
515 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 15, 1996 / Details: COLLIMATORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→40 Å / Num. obs: 6720 / % possible obs: 62.7 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.63
Reflection shellResolution: 1.93→2.01 Å / % possible all: 30
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. obs: 5268 / % possible obs: 73.8 %
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 60.9 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AZP

1azp


Resolution: 2.2→8 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.276 286 5.5 %RANDOM
Rwork0.19 ---
obs-5216 73.8 %-
Displacement parametersBiso mean: 44.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms525 322 0 102 949
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d3.47
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.881.5
X-RAY DIFFRACTIONx_mcangle_it4.872
X-RAY DIFFRACTIONx_scbond_it3.912
X-RAY DIFFRACTIONx_scangle_it5.732.5
LS refinement shellResolution: 2.2→2.33 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 32 4.4 %
Rwork0.33 689 -
obs--62.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM_NDBX_HIGH.DNATOPH11.WAT
X-RAY DIFFRACTION3PARAM11.WATTOP_NDBX.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5.5 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.94
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg3.47
X-RAY DIFFRACTIONx_mcbond_it2.881.5
X-RAY DIFFRACTIONx_scbond_it3.912
X-RAY DIFFRACTIONx_mcangle_it4.872
X-RAY DIFFRACTIONx_scangle_it5.732.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.34 / % reflection Rfree: 4.4 % / Rfactor Rwork: 0.33

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