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- PDB-4e6s: Crystal structure of the SCAN domain from mouse Zfp206 -

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Basic information

Entry
Database: PDB / ID: 4e6s
TitleCrystal structure of the SCAN domain from mouse Zfp206
ComponentsZinc finger and SCAN domain-containing protein 10
KeywordsTRANSCRIPTION / SCAN domain / protein interaction / other SCANs / N-terminal part / zinc finger transcription factor
Function / homology
Function and homology information


stem cell differentiation / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / nucleus / metal ion binding
Similarity search - Function
DNA breaking-rejoining enzymes fold / DNA breaking-rejoining enzymes / SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. ...DNA breaking-rejoining enzymes fold / DNA breaking-rejoining enzymes / SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Zinc finger and SCAN domain-containing protein 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLiang, Y. / Choo, S.H. / Rossbach, M. / Baburajendran, N. / Palasingam, P. / Kolatkar, P.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Crystal optimization and preliminary diffraction data analysis of the SCAN domain of Zfp206.
Authors: Liang, Y. / Choo, S.H. / Rossbach, M. / Baburajendran, N. / Palasingam, P. / Kolatkar, P.R.
History
DepositionMar 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger and SCAN domain-containing protein 10


Theoretical massNumber of molelcules
Total (without water)10,7531
Polymers10,7531
Non-polymers00
Water45025
1
A: Zinc finger and SCAN domain-containing protein 10

A: Zinc finger and SCAN domain-containing protein 10


Theoretical massNumber of molelcules
Total (without water)21,5072
Polymers21,5072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3270 Å2
ΔGint-22 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.565, 67.565, 87.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Zinc finger and SCAN domain-containing protein 10 / Zinc finger protein 206


Mass: 10753.480 Da / Num. of mol.: 1 / Fragment: SCAN domain, UNP RESIDUES 36-128 / Mutation: Q107A, V115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zscan10, Zfp206 / Plasmid: pDEST-HisMBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3URR7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNIPROT. THE AUTHOR ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNIPROT. THE AUTHOR STATES THERE IS A MUTATION Q106A IN THIS PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3247.04
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, hanging drop80.3M ammonium sulfate, 0.1 M Tris-Cl, pH 8.6, 25% PEG 3350, 0.1M EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 291K
2912vapor diffusion, hanging drop80.3M ammonium sulfate, 0.1 M Tris-Cl, pH 8.6, 25% PEG 3350, 0.1M EDTA, Mercury derivative, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.081
SYNCHROTRONNSLS X29A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJun 29, 2009
ADSC QUANTUM 315r2CCDAug 31, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0811
211
ReflectionResolution: 1.85→50 Å / Num. obs: 8995 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 15.2 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 47.538
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 5.976 / Num. unique all: 8995 / Rsym value: 0.468 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→47.776 Å / SU ML: 0.27 / σ(F): 0.15 / Phase error: 21.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 869 10 %
Rwork0.2036 --
obs0.2068 8692 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.354 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1125 Å2-0 Å20 Å2
2---4.1125 Å20 Å2
3---8.2251 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms690 0 0 25 715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008707
X-RAY DIFFRACTIONf_angle_d0.984956
X-RAY DIFFRACTIONf_dihedral_angle_d15.898274
X-RAY DIFFRACTIONf_chiral_restr0.059102
X-RAY DIFFRACTIONf_plane_restr0.006127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8496-1.96550.26271300.2051118991
1.9655-2.11730.2321400.1893124594
2.1173-2.33030.2041450.185129797
2.3303-2.66750.22561430.1942131299
2.6675-3.36060.25241520.2095134999
3.3606-47.79160.23241590.2075143199
Refinement TLS params.Method: refined / Origin x: -21.0351 Å / Origin y: -11.6745 Å / Origin z: -2.4379 Å
111213212223313233
T0.2762 Å2-0.0152 Å2-0.0057 Å2-0.3315 Å2-0.016 Å2--0.3102 Å2
L1.9977 °2-0.2538 °2-0.4029 °2-1.6642 °20.3663 °2--1.0752 °2
S-0.0105 Å °0.2772 Å °0.1185 Å °-0.1139 Å °-0.0751 Å °0.2835 Å °-0.0089 Å °-0.3587 Å °-0 Å °
Refinement TLS groupSelection details: all

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