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- PDB-5d2q: Crystal structure of STPR from Bombyx Mori in complex with 20-bp ... -

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Basic information

Entry
Database: PDB / ID: 5d2q
TitleCrystal structure of STPR from Bombyx Mori in complex with 20-bp DNA derived from +290 site of the fibroin gene
Components
  • DNA (40-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: 2.4 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 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: Fibroin-modulator-binding protein-1
B: DNA (40-MER)


Theoretical massNumber of molelcules
Total (without water)24,3562
Polymers24,3562
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-21 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.890, 45.890, 240.380
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: 12047.971 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 (40-MER)


Mass: 12307.974 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.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% PEG 3350, 16% Glycerol,0.2 M ammonium citrate pH7.0

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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: Mar 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 10911 / % possible obs: 99.8 % / Redundancy: 6 % / Net I/σ(I): 12.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 2.4→45.08 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 24.299 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29595 523 4.8 %RANDOM
Rwork0.24671 ---
obs0.24915 10310 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.413 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å20 Å2-0 Å2
2--2.64 Å2-0 Å2
3----5.28 Å2
Refinement stepCycle: 1 / Resolution: 2.4→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms584 814 0 37 1435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0141510
X-RAY DIFFRACTIONr_bond_other_d0.0050.021042
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.4652205
X-RAY DIFFRACTIONr_angle_other_deg2.2732407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.569577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.4182029
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.41215107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5691513
X-RAY DIFFRACTIONr_chiral_restr0.0950.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021164
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02331
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_it5.1154.473311
X-RAY DIFFRACTIONr_mcbond_other5.0724.472310
X-RAY DIFFRACTIONr_mcangle_it7.5896.672387
X-RAY DIFFRACTIONr_mcangle_other7.5976.678388
X-RAY DIFFRACTIONr_scbond_it4.7013.8851199
X-RAY DIFFRACTIONr_scbond_other4.6983.8841198
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9125.7911818
X-RAY DIFFRACTIONr_long_range_B_refined9.69534.2572006
X-RAY DIFFRACTIONr_long_range_B_other9.69334.2171996
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 37 -
Rwork0.429 724 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
113.828134.5053-4.205686.2-10.49831.280.772-0.31721.34371.1025-0.58953.5384-0.15520.0855-0.18250.74060.089-0.4450.3039-0.23370.59230.52277.369-58.5095
23.6088-4.0961-8.57844.6569.739820.3959-0.19430.2681-0.19140.2041-0.25090.22450.4827-0.63640.44510.2962-0.1321-0.01750.31950.15860.33684.9485-2.4915-55.1175
310.2971-21.4837-12.261546.340620.903929.18150.86920.2408-0.1515-1.8855-0.13450.5716-0.4083-1.3427-0.73470.4517-0.0212-0.15240.1032-0.02220.442110.4318-8.7994-45.8296
40.1397-0.2682-0.068913.12795.59295.193-0.06830.04140.1516-0.59640.236-0.4678-0.11090.2822-0.16770.2092-0.00140.03080.1210.01130.26613.55285.0276-39.1613
58.69544.88660.9522.76180.51381.24820.02110.20720.2318-0.01230.07360.1372-0.0750.0151-0.09470.13620.0763-0.01460.1069-0.00020.2266-1.4515.0754-32.0824
66.12830.99715.21391.7439-1.27887.33280.3557-0.35360.03710.1988-0.4599-0.00490.16030.17780.10420.1844-0.04560.02740.2067-0.04320.3393-11.2146-1.174-22.4203
72.83940.2758-2.22731.15351.26214.74160.03070.16250.3514-0.03060.0679-0.02020.2494-0.2229-0.09860.24360.0357-0.00260.13660.00920.2338-2.28166.6372-29.4965
80.49060.1426-0.67513.81640.65828.1210.04140.11390.31180.06290.4479-0.19690.47970.1593-0.48920.2740.0120.06010.23860.02540.226512.67728.5664-53.3718
91.70340.1492-1.21651.70760.96946.71180.0428-0.0190.16840.10840.0386-0.07480.3055-0.3201-0.08140.08870.00060.00630.08990.01010.2287-5.84917.4338-23.5729
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A113 - 116
2X-RAY DIFFRACTION2A117 - 123
3X-RAY DIFFRACTION3A124 - 128
4X-RAY DIFFRACTION4A129 - 144
5X-RAY DIFFRACTION5A145 - 168
6X-RAY DIFFRACTION6A169 - 189
7X-RAY DIFFRACTION7B-20 - -3
8X-RAY DIFFRACTION8B-2 - 7
9X-RAY DIFFRACTION9B8 - 20

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