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- PDB-5d60: Structure of Chaetomium thermophilum Skn7 coiled-coil domain, cry... -

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Basic information

Entry
Database: PDB / ID: 5d60
TitleStructure of Chaetomium thermophilum Skn7 coiled-coil domain, crystal form III
ComponentsPutative transcription factor
KeywordsTRANSCRIPTION / coiled-coil
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / DNA-binding transcription factor activity / identical protein binding / nucleus
Similarity search - Function
HSF-type DNA-binding domain signature. / Heat shock factor (HSF)-type, DNA-binding / HSF-type DNA-binding / heat shock factor / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcription factor SKN7
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsNeudegger, T. / Verghese, J. / Hayer-Hartl, M. / Hartl, F.U. / Bracher, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structure of human heat-shock transcription factor 1 in complex with DNA.
Authors: Neudegger, T. / Verghese, J. / Hayer-Hartl, M. / Hartl, F.U. / Bracher, A.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / 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: Putative transcription factor
B: Putative transcription factor
C: Putative transcription factor
D: Putative transcription factor


Theoretical massNumber of molelcules
Total (without water)27,7834
Polymers27,7834
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-94 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.730, 40.202, 52.777
Angle α, β, γ (deg.)90.000, 118.570, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA160 - 2131 - 54
21SERSERBB160 - 2131 - 54
12SERSERAA160 - 2131 - 54
22SERSERCC160 - 2131 - 54
13SERSERAA160 - 2131 - 54
23SERSERDD160 - 2131 - 54
14LEULEUBB160 - 2201 - 61
24LEULEUCC160 - 2201 - 61
15LEULEUBB160 - 2201 - 61
25LEULEUDD160 - 2201 - 61
16LEULEUCC160 - 2201 - 61
26LEULEUDD160 - 2201 - 61

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Putative transcription factor / CtSkn7


Mass: 6945.839 Da / Num. of mol.: 4 / Fragment: UNP residues 160-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0048700 / Plasmid: pHUE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0SB31
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 1.7 Å3/Da / Density % sol: 27.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25 % PEG-3350, 0.2 M MgCl2 and 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.923
11-H, -K, H+L20.077
ReflectionResolution: 1.9→44.55 Å / Num. obs: 14684 / % possible obs: 97.8 % / Redundancy: 2.8 % / Biso Wilson estimate: 26.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.048 / Net I/σ(I): 7.2 / Num. measured all: 41428
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.9-1.942.80.5991.725979150.7220.40796.6
9.09-44.552.50.0516.33651440.9990.03592.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D5Y

5d5y


Resolution: 1.9→44.55 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2975 / WRfactor Rwork: 0.2387 / FOM work R set: 0.7883 / SU B: 3.939 / SU ML: 0.12 / SU R Cruickshank DPI: 0.0556 / SU Rfree: 0.0454 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2947 753 5.2 %RANDOM
Rwork0.2405 ---
obs0.2432 13834 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.6 Å2 / Biso mean: 45.994 Å2 / Biso min: 17.98 Å2
Baniso -1Baniso -2Baniso -3
1-31.62 Å20 Å23.69 Å2
2--5.11 Å2-0 Å2
3----36.73 Å2
Refinement stepCycle: final / Resolution: 1.9→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 0 77 1927
Biso mean---44.47 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191852
X-RAY DIFFRACTIONr_bond_other_d0.0090.021846
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.9642495
X-RAY DIFFRACTIONr_angle_other_deg1.79534219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1485234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.75928.49593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6715378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.156154
X-RAY DIFFRACTIONr_chiral_restr0.090.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022174
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02402
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A23050.22
12B23050.22
21A23490.2
22C23490.2
31A22340.25
32D22340.25
41B26220.23
42C26220.23
51B26230.23
52D26230.23
61C25850.25
62D25850.25
LS refinement shellResolution: 1.896→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.566 45 -
Rwork0.473 959 -
all-1004 -
obs--92.45 %

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