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- PDB-3eus: The crystal structure of the DNA binding protein from Silicibacte... -

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Basic information

Entry
Database: PDB / ID: 3eus
TitleThe crystal structure of the DNA binding protein from Silicibacter pomeroyi
ComponentsDNA-binding protein
KeywordsDNA BINDING PROTEIN / STRUCTURAL GENOMICS / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / DNA-binding
Function / homology
Function and homology information


Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-binding protein, putative
Similarity search - Component
Biological speciesSilicibacter pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhang, R. / Li, H. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the DNA binding protein from Silicibacter pomeroyi
Authors: Zhang, R. / Li, H. / Freeman, L. / Joachimiak, A.
History
DepositionOct 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein
B: DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)19,3982
Polymers19,3982
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-19 kcal/mol
Surface area8230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.164, 60.641, 68.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein existed as dimer. The deposited MolA/MolB represent the dimer in the asymmetric unit.

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Components

#1: Protein DNA-binding protein


Mass: 9699.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Strain: DSS-3 / Gene: GI:56696110, SPO1217 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5LU41
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20% W/V PEG1000, 0.1M phosphate-citrate, 0.2M Li2SO4, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2007 / Details: mirrors
RadiationMonochromator: 0.9794 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→45.41 Å / Num. all: 15276 / Num. obs: 15172 / % possible obs: 99.32 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.9
Reflection shellResolution: 1.8→1.847 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 1.36 / Num. unique all: 1168 / % possible all: 95.29

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→45.41 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.947 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.139 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25375 800 5 %RANDOM
Rwork0.20099 ---
obs0.20351 15172 99.32 %-
all-15276 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.854 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 0 88 1370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221303
X-RAY DIFFRACTIONr_bond_other_d0.0010.02915
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9661758
X-RAY DIFFRACTIONr_angle_other_deg1.01732209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9135162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52122.81264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29715242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0411518
X-RAY DIFFRACTIONr_chiral_restr0.1040.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02272
X-RAY DIFFRACTIONr_mcbond_it0.9881.5812
X-RAY DIFFRACTIONr_mcbond_other0.2831.5326
X-RAY DIFFRACTIONr_mcangle_it1.76521302
X-RAY DIFFRACTIONr_scbond_it3.0063491
X-RAY DIFFRACTIONr_scangle_it4.9044.5456
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 56 -
Rwork0.332 1057 -
obs-1113 95.29 %
Refinement TLS params.Method: refined / Origin x: 6.212 Å / Origin y: 40.995 Å / Origin z: 11.745 Å
111213212223313233
T0.0136 Å20.012 Å20.0395 Å2-0.0749 Å20.0506 Å2--0.1375 Å2
L2.0648 °20.7965 °20.3248 °2-3.554 °20.29 °2--2.172 °2
S-0.0089 Å °0.0479 Å °0.1163 Å °0.0392 Å °0.0966 Å °0.1924 Å °0.0093 Å °0.0718 Å °-0.0876 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 40
2X-RAY DIFFRACTION1A41 - 83
3X-RAY DIFFRACTION1B6 - 40
4X-RAY DIFFRACTION1B41 - 82

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