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- PDB-6j5b: Structural basis for the target DNA recognition and binding by th... -

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Basic information

Entry
Database: PDB / ID: 6j5b
TitleStructural basis for the target DNA recognition and binding by the MYB domain of phosphate starvation response regulator 1
Components
  • DNA (5'-D(*GP*GP*TP*AP*CP*AP*GP*TP*AP*TP*AP*TP*AP*CP*CP*AP*TP*AP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*AP*TP*GP*GP*TP*AP*TP*AP*TP*AP*CP*TP*GP*TP*AP*CP*C)-3')
  • Protein PHOSPHATE STARVATION RESPONSE 1
KeywordsTRANSCRIPTION/DNA / MYB domain DNA / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


response to arsenite ion / sulfate ion homeostasis / cellular response to high light intensity / cellular response to phosphate starvation / regulation of monoatomic ion transmembrane transport / circadian rhythm / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
: / MYB-CC type transcription factor, LHEQLE-containing domain / MYB-CC type transfactor, LHEQLE motif / Myb domain, plants / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily ...: / MYB-CC type transcription factor, LHEQLE-containing domain / MYB-CC type transfactor, LHEQLE motif / Myb domain, plants / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein PHOSPHATE STARVATION RESPONSE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsJiang, M.Q. / Sun, L.F. / Isupov, M.N. / Wu, Y.K.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31470741 China
CitationJournal: Febs J. / Year: 2019
Title: Structural basis for the Target DNA recognition and binding by the MYB domain of phosphate starvation response 1.
Authors: Jiang, M. / Sun, L. / Isupov, M.N. / Littlechild, J.A. / Wu, X. / Wang, Q. / Wang, Q. / Yang, W. / Wu, Y.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein PHOSPHATE STARVATION RESPONSE 1
B: DNA (5'-D(*GP*GP*TP*AP*CP*AP*GP*TP*AP*TP*AP*TP*AP*CP*CP*AP*TP*AP*AP*A)-3')
C: Protein PHOSPHATE STARVATION RESPONSE 1
D: Protein PHOSPHATE STARVATION RESPONSE 1
E: DNA (5'-D(*GP*GP*TP*AP*CP*AP*GP*TP*AP*TP*AP*TP*AP*CP*CP*AP*TP*AP*AP*A)-3')
F: Protein PHOSPHATE STARVATION RESPONSE 1
G: DNA (5'-D(*TP*TP*TP*AP*TP*GP*GP*TP*AP*TP*AP*TP*AP*CP*TP*GP*TP*AP*CP*C)-3')
H: Protein PHOSPHATE STARVATION RESPONSE 1
I: DNA (5'-D(*GP*GP*TP*AP*CP*AP*GP*TP*AP*TP*AP*TP*AP*CP*CP*AP*TP*AP*AP*A)-3')
J: Protein PHOSPHATE STARVATION RESPONSE 1
K: DNA (5'-D(*TP*TP*TP*AP*TP*GP*GP*TP*AP*TP*AP*TP*AP*CP*TP*GP*TP*AP*CP*C)-3')
U: DNA (5'-D(*TP*TP*TP*AP*TP*GP*GP*TP*AP*TP*AP*TP*AP*CP*TP*GP*TP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)78,26412
Polymers78,26412
Non-polymers00
Water00
1
A: Protein PHOSPHATE STARVATION RESPONSE 1
B: DNA (5'-D(*GP*GP*TP*AP*CP*AP*GP*TP*AP*TP*AP*TP*AP*CP*CP*AP*TP*AP*AP*A)-3')
D: Protein PHOSPHATE STARVATION RESPONSE 1
U: DNA (5'-D(*TP*TP*TP*AP*TP*GP*GP*TP*AP*TP*AP*TP*AP*CP*TP*GP*TP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)26,0884
Polymers26,0884
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-24 kcal/mol
Surface area13050 Å2
MethodPISA
2
C: Protein PHOSPHATE STARVATION RESPONSE 1
E: DNA (5'-D(*GP*GP*TP*AP*CP*AP*GP*TP*AP*TP*AP*TP*AP*CP*CP*AP*TP*AP*AP*A)-3')
F: Protein PHOSPHATE STARVATION RESPONSE 1
G: DNA (5'-D(*TP*TP*TP*AP*TP*GP*GP*TP*AP*TP*AP*TP*AP*CP*TP*GP*TP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)26,0884
Polymers26,0884
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-26 kcal/mol
Surface area13080 Å2
MethodPISA
3
H: Protein PHOSPHATE STARVATION RESPONSE 1
I: DNA (5'-D(*GP*GP*TP*AP*CP*AP*GP*TP*AP*TP*AP*TP*AP*CP*CP*AP*TP*AP*AP*A)-3')
J: Protein PHOSPHATE STARVATION RESPONSE 1
K: DNA (5'-D(*TP*TP*TP*AP*TP*GP*GP*TP*AP*TP*AP*TP*AP*CP*TP*GP*TP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)26,0884
Polymers26,0884
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-27 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.581, 53.581, 98.884
Angle α, β, γ (deg.)91.470, 91.470, 94.790
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22D
13A
23F
14A
24H
15A
25J
16B
26E
17B
27I
18C
28D
19C
29F
110C
210H
111C
211J
112D
212F
113D
213H
114D
214J
115E
215I
116F
216H
117F
217J
118G
218K
119G
219U
120H
220J
121K
221U

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAARGARGAA226 - 2813 - 58
21ALAALAARGARGCC226 - 2813 - 58
12ALAALATYRTYRAA226 - 2823 - 59
22ALAALATYRTYRDD226 - 2823 - 59
13ALAALAARGARGAA226 - 2813 - 58
23ALAALAARGARGFF226 - 2813 - 58
14ALAALAARGARGAA226 - 2813 - 58
24ALAALAARGARGHH226 - 2813 - 58
15ALAALAARGARGAA226 - 2813 - 58
25ALAALAARGARGJJ226 - 2813 - 58
16DGDGDADABB1 - 201 - 20
26DGDGDADAEE1 - 201 - 20
17DGDGDADABB1 - 201 - 20
27DGDGDADAII1 - 201 - 20
18ALAALAARGARGCC226 - 2813 - 58
28ALAALAARGARGDD226 - 2813 - 58
19LYSLYSARGARGCC225 - 2812 - 58
29LYSLYSARGARGFF225 - 2812 - 58
110LYSLYSARGARGCC225 - 2812 - 58
210LYSLYSARGARGHH225 - 2812 - 58
111ALAALAARGARGCC226 - 2813 - 58
211ALAALAARGARGJJ226 - 2813 - 58
112ALAALAARGARGDD226 - 2813 - 58
212ALAALAARGARGFF226 - 2813 - 58
113ALAALAARGARGDD226 - 2813 - 58
213ALAALAARGARGHH226 - 2813 - 58
114ALAALAARGARGDD226 - 2813 - 58
214ALAALAARGARGJJ226 - 2813 - 58
115DGDGDADAEE1 - 201 - 20
215DGDGDADAII1 - 201 - 20
116LYSLYSTYRTYRFF225 - 2822 - 59
216LYSLYSTYRTYRHH225 - 2822 - 59
117ALAALAARGARGFF226 - 2813 - 58
217ALAALAARGARGJJ226 - 2813 - 58
118DTDTDCDCGG1 - 201 - 20
218DTDTDCDCKK1 - 201 - 20
119DTDTDCDCGG1 - 201 - 20
219DTDTDCDCUL1 - 201 - 20
120ALAALAARGARGHH226 - 2813 - 58
220ALAALAARGARGJJ226 - 2813 - 58
121DTDTDCDCKK1 - 201 - 20
221DTDTDCDCUL1 - 201 - 20

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

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Components

#1: Protein
Protein PHOSPHATE STARVATION RESPONSE 1 / AtPHR1


Mass: 6912.077 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHR1, At4g28610, T5F17.60 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q94CL7
#2: DNA chain DNA (5'-D(*GP*GP*TP*AP*CP*AP*GP*TP*AP*TP*AP*TP*AP*CP*CP*AP*TP*AP*AP*A)-3')


Mass: 6150.031 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*TP*TP*AP*TP*GP*GP*TP*AP*TP*AP*TP*AP*CP*TP*GP*TP*AP*CP*C)-3')


Mass: 6113.975 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 3.51 Å3/Da / Density % sol: 64.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30% PEG 3350, 0.2M CaCl2, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.7→47.52 Å / Num. obs: 29308 / % possible obs: 97.5 % / Redundancy: 2.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.052 / Rrim(I) all: 0.09 / Net I/σ(I): 7.7 / Num. measured all: 78501 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.830.3113978438460.1932.2763.880.495.6
8.95-47.520.02519617750.9980.0180.03137.395.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
PHENIXphasing
RefinementResolution: 2.7→39.44 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 18.211 / SU ML: 0.326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.556 / ESU R Free: 0.307
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 1473 5.2 %RANDOM
Rwork0.2178 ---
obs0.2195 27093 95.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 222.79 Å2 / Biso mean: 99.649 Å2 / Biso min: 54.37 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-1.41 Å2-8.39 Å2
2---0.85 Å2-8.45 Å2
3---3.1 Å2
Refinement stepCycle: final / Resolution: 2.7→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 2442 0 0 5214
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0115564
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.4038008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6945341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18518.69145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.31115536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.31530
X-RAY DIFFRACTIONr_chiral_restr0.0830.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023338
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A17380.07
12C17380.07
21A17650.07
22D17650.07
31A17060.08
32F17060.08
41A17280.08
42H17280.08
51A16990.09
52J16990.09
61B18120.06
62E18120.06
71B18090.06
72I18090.06
81C17400.05
82D17400.05
91C17480.06
92F17480.06
101C17590.05
102H17590.05
111C17110.08
112J17110.08
121D17120.07
122F17120.07
131D17340.05
132H17340.05
141D17040.08
142J17040.08
151E18200.06
152I18200.06
161F17390.08
162H17390.08
171F17280.07
172J17280.07
181G17780.06
182K17780.06
191G17460.08
192U17460.08
201H16990.08
202J16990.08
211K17650.06
212U17650.06
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 94 -
Rwork0.426 1700 -
all-1794 -
obs--82.33 %

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