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- PDB-4koo: Crystal Structure of WHY1 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 4koo
TitleCrystal Structure of WHY1 from Arabidopsis thaliana
ComponentsSingle-stranded DNA-binding protein WHY1, chloroplastic
KeywordsDNA BINDING PROTEIN / Plant / Whirly / SINGLE-STRANDED DNA BINDING PROTEIN
Function / homology
Function and homology information


plastid chromosome / chloroplast nucleoid / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / chloroplast / defense response / single-stranded DNA binding / DNA repair / mRNA binding / regulation of DNA-templated transcription ...plastid chromosome / chloroplast nucleoid / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / chloroplast / defense response / single-stranded DNA binding / DNA repair / mRNA binding / regulation of DNA-templated transcription / DNA binding / extracellular region
Similarity search - Function
Whirly transcription factor / Whirly transcription factor / Transcriptional Coactivator Pc4; Chain A / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Single-stranded DNA-binding protein WHY1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsCappadocia, L. / Parent, J.S. / Brisson, N. / Sygusch, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: A family portrait: structural comparison of the Whirly proteins from Arabidopsis thaliana and Solanum tuberosum.
Authors: Cappadocia, L. / Parent, J.S. / Sygusch, J. / Brisson, N.
History
DepositionMay 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single-stranded DNA-binding protein WHY1, chloroplastic
B: Single-stranded DNA-binding protein WHY1, chloroplastic
C: Single-stranded DNA-binding protein WHY1, chloroplastic
D: Single-stranded DNA-binding protein WHY1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,35712
Polymers80,0324
Non-polymers1,3258
Water11,908661
1
A: Single-stranded DNA-binding protein WHY1, chloroplastic
B: Single-stranded DNA-binding protein WHY1, chloroplastic
hetero molecules

A: Single-stranded DNA-binding protein WHY1, chloroplastic
B: Single-stranded DNA-binding protein WHY1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,51014
Polymers80,0324
Non-polymers1,47910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area12940 Å2
ΔGint-89 kcal/mol
Surface area32810 Å2
MethodPISA
2
C: Single-stranded DNA-binding protein WHY1, chloroplastic
D: Single-stranded DNA-binding protein WHY1, chloroplastic
hetero molecules

C: Single-stranded DNA-binding protein WHY1, chloroplastic
D: Single-stranded DNA-binding protein WHY1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,20310
Polymers80,0324
Non-polymers1,1716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area13970 Å2
ΔGint-81 kcal/mol
Surface area33730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.592, 180.685, 116.069
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Single-stranded DNA-binding protein WHY1, chloroplastic / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 1 / Protein WHIRLY 1 / AtWHY1


Mass: 20007.902 Da / Num. of mol.: 4 / Fragment: UNP residues 74-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col-0 / Gene: At1g14410, F14L17.18, PTAC1, WHY1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9M9S3
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 5% PEG 3350, 0.2M Potassium Acetate, 0.1M MES pH5.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 69860 / Num. obs: 69721 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.048 / Χ2: 1.058 / Net I/σ(I): 19.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.88-1.956.50.30868650.957199.2
1.95-2.036.80.2269031.012199.8
2.03-2.126.90.15468961.02199.9
2.12-2.2370.12169061.042199.9
2.23-2.377.10.08969441.1141100
2.37-2.557.30.0769541.1481100
2.55-2.817.50.05169621.3111100
2.81-3.217.50.04169911.0231100
3.21-4.057.40.03870530.961100
4.05-507.20.0372470.974199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→30.276 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8551 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 1999 2.87 %RANDOM
Rwork0.1758 ---
obs0.1769 69666 99.67 %-
all-69721 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.59 Å2 / Biso mean: 35.8517 Å2 / Biso min: 8 Å2
Refinement stepCycle: LAST / Resolution: 1.88→30.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5346 0 78 661 6085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125611
X-RAY DIFFRACTIONf_angle_d1.3637609
X-RAY DIFFRACTIONf_chiral_restr0.088810
X-RAY DIFFRACTIONf_plane_restr0.006960
X-RAY DIFFRACTIONf_dihedral_angle_d16.2092031
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-1.92720.29741380.2264655479397
1.9272-1.97930.21321420.200747944936100
1.9793-2.03760.24191410.18847794920100
2.0376-2.10330.23411410.171848104951100
2.1033-2.17850.20171420.173447794921100
2.1785-2.26570.21551420.169348074949100
2.2657-2.36870.22111430.166848234966100
2.3687-2.49360.21791420.175148334975100
2.4936-2.64970.23211430.174548164959100
2.6497-2.85410.23091430.171148464989100
2.8541-3.14110.22891440.174748725016100
3.1411-3.5950.1691440.163948665010100
3.595-4.52690.20341460.158949245070100
4.5269-30.2760.21621480.19745063521199

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