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- PDB-5d23: The crystal structure of STPR from Bombyx mori in complex with 13... -

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Basic information

Entry
Database: PDB / ID: 5d23
TitleThe crystal structure of STPR from Bombyx mori in complex with 13-bp DNA derived from the +290 site of fibroin gene
Components
  • DNA (26-MER)
  • Fibroin-modulator-binding protein-1
KeywordsTRANSCRIPTION/DNA / Protein-DNA complex / All a-helix / Major groove binding pattern / 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: 1.95 Å
AuthorsCheng, W.
Funding support China, 1items
OrganizationGrant numberCountry
China
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 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Fibroin-modulator-binding protein-1
B: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)20,0322
Polymers20,0322
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-23 kcal/mol
Surface area8780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.180, 123.180, 73.574
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-211-

HOH

21A-229-

HOH

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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 (26-MER)


Mass: 7984.202 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.: 92 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15% PEG4000, 20% 2-propanol, 0.1M 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: Oct 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 15446 / % possible obs: 98.2 % / Redundancy: 4.6 % / Net I/σ(I): 12.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing
RefinementResolution: 1.95→27.45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.537 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23192 774 5 %RANDOM
Rwork0.20483 ---
obs0.20616 14672 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.583 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0.45 Å20 Å2
2---0.9 Å20 Å2
3---2.92 Å2
Refinement stepCycle: 1 / Resolution: 1.95→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms508 527 0 92 1127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0151101
X-RAY DIFFRACTIONr_bond_other_d0.0010.02821
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.5251587
X-RAY DIFFRACTIONr_angle_other_deg1.20931884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.221563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.06417.625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9441591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5071514
X-RAY DIFFRACTIONr_chiral_restr0.0620.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02254
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_it1.583.086255
X-RAY DIFFRACTIONr_mcbond_other1.5673.077254
X-RAY DIFFRACTIONr_mcangle_it2.5034.609317
X-RAY DIFFRACTIONr_mcangle_other2.54.618318
X-RAY DIFFRACTIONr_scbond_it1.6412.7845
X-RAY DIFFRACTIONr_scbond_other1.6422.701844
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5334.0251270
X-RAY DIFFRACTIONr_long_range_B_refined6.31724.7871481
X-RAY DIFFRACTIONr_long_range_B_other6.16124.1631432
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 59 -
Rwork0.277 1081 -
obs--99.04 %
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)
148.2355-18.162657.177892.4499-55.781781.4850.9237-0.0584-0.7491-3.1082-0.5631-1.07392.23170.2263-0.36061.07550.37780.41461.518-0.27270.554514.405-21.089-23.012
29.6927.88285.311713.9488-2.26878.6799-0.14740.9157-0.667-0.5975-0.1898-1.31230.34731.34090.33720.1264-0.03890.220.407-0.07240.416713.841-19.894-17.212
313.27347.1572-10.73599.37692.828522.14380.0381-0.9466-0.95240.0778-0.6066-0.65890.07360.60370.56860.0242-0.03270.06470.18570.03170.30079.048-18.234-7.35
417.0245-7.2829-2.125812.2314-4.44044.1897-0.0842-0.6528-0.4750.8496-0.2568-0.5137-0.47450.55870.3410.2025-0.2038-0.0940.29990.05960.11251.248-16.4672.376
58.37961.83386.82995.07910.57328.8279-0.0707-0.44640.1254-0.2114-0.27120.1066-0.5653-0.00720.34180.2339-0.10890.00520.1345-0.03630.1309-6.326-13.308-7.841
67.20066.35963.153910.51211.635317.3867-0.77750.13080.4303-0.98040.40250.4703-0.82770.55110.3750.5227-0.058-0.2170.03660.0310.239-16.208-13.974-23.446
72.0197-0.591.971414.1372-5.6053.7355-0.36990.11130.1807-1.03640.3540.41390.0484-0.02970.01580.3639-0.0852-0.08950.0946-0.00520.1358-18.523-22.563-25.155
81.276-3.0822.197522.564-6.25347.1684-0.1599-0.03320.02890.33730.2733-0.47860.01840.1583-0.11340.17850.022-0.02370.1028-0.05210.0674-13.601-33.545-19.978
95.60184.44791.07553.85890.79911.7013-0.37080.2232-0.3133-0.54340.3081-0.2707-0.1080.26240.06270.2279-0.10390.03620.1975-0.07560.1558-5.331-19.127-14.499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A127 - 129
2X-RAY DIFFRACTION2A130 - 134
3X-RAY DIFFRACTION3A135 - 142
4X-RAY DIFFRACTION4A143 - 148
5X-RAY DIFFRACTION5A149 - 163
6X-RAY DIFFRACTION6A164 - 172
7X-RAY DIFFRACTION7A173 - 178
8X-RAY DIFFRACTION8A179 - 190
9X-RAY DIFFRACTION9B-17 - 17

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