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- PDB-1udv: Crystal structure of the hyperthermophilic archaeal dna-binding p... -

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Basic information

Entry
Database: PDB / ID: 1udv
TitleCrystal structure of the hyperthermophilic archaeal dna-binding protein Sso10b2 at 1.85 A
ComponentsDNA binding protein SSO10b
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


chromosome condensation / chromosome / double-stranded DNA binding / RNA binding / cytoplasm
Similarity search - Function
DNA/RNA-binding protein Alba / Alba-like domain / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA/RNA-binding protein Alba 2
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsChou, C.-C. / Lin, T.-W. / Chen, C.-Y. / Wang, A.H.J.
CitationJournal: J.BACTERIOL. / Year: 2003
Title: Crystal structure of the hyperthermophilic archaeal DNA-binding protein Sso10b2 at a resolution of 1.85 Angstroms
Authors: Chou, C.C. / Lin, T.W. / Chen, C.Y. / Wang, A.H.J.
History
DepositionMay 7, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA binding protein SSO10b
B: DNA binding protein SSO10b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5773
Polymers20,5122
Non-polymers651
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-37 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.020, 134.980, 35.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-296-

HOH

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Components

#1: Protein DNA binding protein SSO10b / SSO10B2


Mass: 10255.882 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Cellular location: CYTOPLASM / Gene: SSO6877 / Plasmid: PET30 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97ZF4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: PEG MME 550, ZnSO4, MES, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
225 %PEG550 MME1reservoir
310 mM1reservoirZnSO4
4100 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.1163 / Wavelength: 1.1163 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 15, 2003 / Details: MIRROR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1163 Å / Relative weight: 1
ReflectionResolution: 1.85→31.78 Å / Num. all: 15639 / Num. obs: 15639 / % possible obs: 99.5 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.9
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1536 / % possible all: 97.6
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 92.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.85→31.78 Å / Rfactor Rfree error: 0.01 / Data cutoff high rms absF: 1000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.274 717 4.9 %RANDOM
Rwork0.239 ---
obs0.239 14610 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.1562 Å2 / ksol: 0.354406 e/Å3
Displacement parametersBiso mean: 34.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.85→31.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 1 150 1559
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.642
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.242.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 97 4.7 %
Rwork0.28 1949 -
obs--79.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.65

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