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- PDB-5d2s: Crystal structure of STPR from Bombyx mori in complex with 18-bp ... -

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Basic information

Entry
Database: PDB / ID: 5d2s
TitleCrystal structure of STPR from Bombyx mori in complex with 18-bp DNA containing four repetitive units of ATAC
Components
  • DNA (36-MER)
  • Fibroin-modulator-binding protein-1
KeywordsTRANSCRIPTION/DNA / Protein-DNA complex / All a-helix / DNA major groove binding / TRANSCRIPTION-DNA complex
Function / homology: / STPRs (score and three amino acid peptide repeats) / DNA / DNA (> 10) / Fibroin-modulator-binding protein-1
Function and homology information
Biological speciesBombyx mori (domestic silkworm)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsCheng, W.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structures of an all-alpha protein running along the DNA major groove.
Authors: Yu, L.Y. / Cheng, W. / Zhou, K. / Li, W.F. / Yu, H.M. / Gao, X. / Shen, X. / Wu, Q. / Chen, Y. / Zhou, C.Z.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibroin-modulator-binding protein-1
B: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)22,8872
Polymers22,8872
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-29 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.011, 44.011, 237.869
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Fibroin-modulator-binding protein-1 / Uncharacterized protein


Mass: 11813.495 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 99-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: fmbp-1, Fmbp-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5FBS0
#2: DNA chain DNA (36-MER)


Mass: 11073.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 18% PEG 2000, 0.1 M sodium citrate pH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 22628 / % possible obs: 99.1 % / Redundancy: 3.2 % / Net I/σ(I): 14.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 2.2→43.28 Å / Cor.coef. Fo:Fc: 0.718 / Cor.coef. Fo:Fc free: 0.389 / SU B: 6.074 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25324 643 5.1 %RANDOM
Rwork0.22672 ---
obs0.22808 11993 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.527 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 2.2→43.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms726 732 0 72 1530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0151551
X-RAY DIFFRACTIONr_bond_other_d0.0010.021146
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.5242236
X-RAY DIFFRACTIONr_angle_other_deg1.30132644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.661590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.2412038
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52615145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.181517
X-RAY DIFFRACTIONr_chiral_restr0.0870.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021257
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02352
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3593.947363
X-RAY DIFFRACTIONr_mcbond_other3.3573.942362
X-RAY DIFFRACTIONr_mcangle_it4.2285.901452
X-RAY DIFFRACTIONr_mcangle_other4.2255.908453
X-RAY DIFFRACTIONr_scbond_it4.1964.2091188
X-RAY DIFFRACTIONr_scbond_other4.1954.2091189
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7246.2391785
X-RAY DIFFRACTIONr_long_range_B_refined7.00738.5067039
X-RAY DIFFRACTIONr_long_range_B_other7.00638.5057015
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 35 -
Rwork0.282 836 -
obs--99.2 %

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