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- PDB-6luk: Crystal structure of the SAMD1 SAM domain in another crystal form -

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Basic information

Entry
Database: PDB / ID: 6luk
TitleCrystal structure of the SAMD1 SAM domain in another crystal form
ComponentsAtherin
KeywordsDNA BINDING PROTEIN / CpG-islands / transcription / decamer
Function / homology
Function and homology information


lipoprotein lipid oxidation / foam cell differentiation / regulation of DNA methylation-dependent heterochromatin formation / low-density lipoprotein particle binding / protein homooligomerization / chromosome / chromatin organization / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding ...lipoprotein lipid oxidation / foam cell differentiation / regulation of DNA methylation-dependent heterochromatin formation / low-density lipoprotein particle binding / protein homooligomerization / chromosome / chromatin organization / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular space / nucleus
Similarity search - Function
: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Sterile alpha motif domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.054 Å
AuthorsCao, Y. / Zhou, Y. / Wang, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870725 China
National Natural Science Foundation of China (NSFC)31570729 China
CitationJournal: Sci Adv / Year: 2021
Title: The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands.
Authors: Stielow, B. / Zhou, Y. / Cao, Y. / Simon, C. / Pogoda, H.M. / Jiang, J. / Ren, Y. / Phanor, S.K. / Rohner, I. / Nist, A. / Stiewe, T. / Hammerschmidt, M. / Shi, Y. / Bulyk, M.L. / Wang, Z. / Liefke, R.
History
DepositionJan 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Atherin
B: Atherin
C: Atherin
D: Atherin
E: Atherin
F: Atherin
G: Atherin
H: Atherin
I: Atherin
J: Atherin
K: Atherin
L: Atherin
M: Atherin
N: Atherin
O: Atherin
P: Atherin
Q: Atherin
R: Atherin
S: Atherin
T: Atherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,94738
Polymers156,21820
Non-polymers1,72918
Water15,006833
1
A: Atherin
B: Atherin
C: Atherin
D: Atherin
E: Atherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,53510
Polymers39,0545
Non-polymers4805
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-104 kcal/mol
Surface area16240 Å2
MethodPISA
2
F: Atherin
G: Atherin
H: Atherin
I: Atherin
J: Atherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4399
Polymers39,0545
Non-polymers3844
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-91 kcal/mol
Surface area16210 Å2
MethodPISA
3
K: Atherin
L: Atherin
M: Atherin
N: Atherin
O: Atherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4399
Polymers39,0545
Non-polymers3844
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-86 kcal/mol
Surface area16120 Å2
MethodPISA
4
P: Atherin
Q: Atherin
R: Atherin
S: Atherin
T: Atherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,53510
Polymers39,0545
Non-polymers4805
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-103 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.430, 182.842, 66.971
Angle α, β, γ (deg.)90.000, 93.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Atherin / Sterile alpha motif domain-containing protein 1 / SAM domain-containing protein 1


Mass: 7810.881 Da / Num. of mol.: 20 / Fragment: SAM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMD1 / Production host: Escherichia Coli BL21(DE3) (bacteria) / References: UniProt: Q6SPF0
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 833 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M bis-tris (pH 7.5), 2.1M ammonium sulphate

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.054→50 Å / Num. obs: 98440 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 12.1
Reflection shellResolution: 2.054→2.12 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8178

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A model solved by Se-Met labelled sample.

Resolution: 2.054→45.71 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.88
RfactorNum. reflection% reflection
Rfree0.2259 4904 4.99 %
Rwork0.1852 --
obs0.1872 98371 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.84 Å2 / Biso mean: 27.0811 Å2 / Biso min: 13.08 Å2
Refinement stepCycle: final / Resolution: 2.054→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11000 0 90 833 11923
Biso mean--43.36 33.55 -
Num. residues----1380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0543-2.07760.30721600.2493273987
2.0776-2.10210.26261620.22733087100
2.1021-2.12770.25821620.21193143100
2.1277-2.15460.25751530.20523154100
2.1546-2.1830.24821800.20653079100
2.183-2.21290.25251440.20533171100
2.2129-2.24450.28981640.20793113100
2.2445-2.2780.24931320.19843119100
2.278-2.31360.25031690.20453173100
2.3136-2.35150.25261720.20593095100
2.3515-2.39210.24691490.20013137100
2.3921-2.43560.26031520.19893120100
2.4356-2.48240.24291600.20413151100
2.4824-2.53310.24031490.19993084100
2.5331-2.58810.2561690.19363127100
2.5881-2.64830.24111750.18873131100
2.6483-2.71460.2171920.19933084100
2.7146-2.78790.24691490.19853182100
2.7879-2.870.23261730.19833107100
2.87-2.96260.25381750.20463106100
2.9626-3.06850.23781380.2083146100
3.0685-3.19130.24651820.20263139100
3.1913-3.33650.25231550.19683145100
3.3365-3.51230.21561720.19373116100
3.5123-3.73230.20431700.16183130100
3.7323-4.02030.18161640.1513109100
4.0203-4.42460.17591670.14243176100
4.4246-5.06410.19711600.15563120100
5.0641-6.37750.25181720.19233126100
6.3775-45.710.1841830.1637315899

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