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- PDB-3hm5: SANT domain of human DNA methyltransferase 1 associated protein 1 -

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Basic information

Entry
Database: PDB / ID: 3hm5
TitleSANT domain of human DNA methyltransferase 1 associated protein 1
ComponentsDNA methyltransferase 1-associated protein 1
KeywordsTRANSCRIPTION / DNA methylation / chromatin / Structural Genomics Consortium / SGC / Activator / Chromatin regulator / Coiled coil / Growth regulation / Nucleus / Phosphoprotein / Repressor / Transcription regulation
Function / homology
Function and homology information


Swr1 complex / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / replication fork / positive regulation of protein import into nucleus / transcription corepressor activity / nucleosome / HATs acetylate histones / regulation of apoptotic process ...Swr1 complex / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / replication fork / positive regulation of protein import into nucleus / transcription corepressor activity / nucleosome / HATs acetylate histones / regulation of apoptotic process / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / regulation of cell cycle / chromatin remodeling / DNA repair / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
DNA methyltransferase 1-associated 1 / DNA methyltransferase 1-associated protein 1 (DMAP1) / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA methyltransferase 1-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsDombrovski, L. / Tempel, W. / Amaya, M.F. / Tong, Y. / Ni, S. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Dombrovski, L. / Tempel, W. / Amaya, M.F. / Tong, Y. / Ni, S. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Park, H. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: SANT domain of human DNA methyltransferase 1 associated protein 1
Authors: Dombrovski, L. / Tempel, W. / Amaya, M.F. / Tong, Y. / Ni, S. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Park, H. / Wu, H.
History
DepositionMay 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_conn.ptnr2_label_seq_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: DNA methyltransferase 1-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2577
Polymers11,2171
Non-polymers406
Water66737
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.523, 36.523, 230.506
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-4-

UNX

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Components

#1: Protein DNA methyltransferase 1-associated protein 1 / DNMT1-associated protein 1 / DNMAP1


Mass: 11216.549 Da / Num. of mol.: 1 / Fragment: SANT domain, UNP residues 121-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DMAP1, KIAA1425 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R / References: UniProt: Q9NPF5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 0.2M calcium chloride, 0.1M HEPES, pH 7.0, vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B10.91987
SYNCHROTRONCLSI 08ID-121.07221
SYNCHROTRONCLSI 08ID-131.00645
Detector
TypeIDDetectorDate
MAR scanner 300 mm plate1IMAGE PLATEApr 6, 2009
MAR scanner 300 mm plate2IMAGE PLATEMay 17, 2009
MAR scanner 300 mm plate3IMAGE PLATEMay 16, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.919871
21.072211
31.006451
Reflection

Av σ(I) over netI: 44.47 / D res high: 2.8 Å / D res low: 30 Å

Redundancy (%)IDNumberRmerge(I) obsΧ2Num. obs% possible obs
7.613009950.0581.6639689100
12.122591960.0611.762138998.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.023099.910.0392.1887.8
4.786.0210010.0512.5157.7
4.184.7810010.052.1157.8
3.84.1810010.0551.7877.8
3.533.810010.0671.8127.8
3.323.5310010.0841.4067.8
3.153.3210010.1121.2517.8
3.023.1510010.1861.1327.7
2.93.0210010.2821.1497.3
2.82.999.610.3651.0866.2
6.023099.920.0352.02513.2
4.786.0210020.0462.04413.9
4.184.7810020.0522.03214.1
3.84.1810020.0711.82914
3.533.810020.1042.05813.7
3.323.5310020.151.68613.5
3.153.3210020.211.46113.3
3.023.1510020.3641.24912.4
2.93.0299.520.4991.218
2.82.988.320.5161.0643.6
ReflectionResolution: 1.8→40 Å / Num. obs: 9198 / % possible obs: 96.8 % / Redundancy: 17 % / Rmerge(I) obs: 0.079 / Χ2: 1.434 / Net I/σ(I): 44.467
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.866.20.476930.77275.6
1.86-1.9410.60.3648330.79592.8
1.94-2.0315.50.3189120.84999.2
2.03-2.1319.20.2338970.96999.9
2.13-2.27200.1689331.139100
2.27-2.4420.10.1419301.4100
2.44-2.6919.90.1159321.387100
2.69-3.0819.60.089601.602100
3.08-3.8818.70.0639802.50199.8
3.88-4016.70.04211281.88499.3

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVEphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→19.905 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.213 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 2.851 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. Structure was solved in I4122 spacegroup using SIRAS, using a thimerosal-soaked sample as "native" and a ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. Structure was solved in I4122 spacegroup using SIRAS, using a thimerosal-soaked sample as "native" and a tetrabromoplatinate derivative. DM and RESOLVE were used for NCS averaging after a rough outline of the protein chain was traced in the initial map. Preliminary model was placed into refinement space group using PHASER. The model was automatically updated with ARP/WARP and further refined/validated wit REFMAC/MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 433 4.769 %RANDOM
Rwork0.223 ---
obs0.225 9080 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 53.98 Å2 / Biso mean: 17.685 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.121 Å20.06 Å20 Å2
2--0.121 Å20 Å2
3----0.181 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms644 0 6 37 687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021665
X-RAY DIFFRACTIONr_bond_other_d0.0010.02441
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.905905
X-RAY DIFFRACTIONr_angle_other_deg0.9631050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.521576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.83622.19541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33615101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.197157
X-RAY DIFFRACTIONr_chiral_restr0.0970.293
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02167
X-RAY DIFFRACTIONr_mcbond_it1.081.5379
X-RAY DIFFRACTIONr_mcbond_other0.3021.5149
X-RAY DIFFRACTIONr_mcangle_it1.9272608
X-RAY DIFFRACTIONr_scbond_it2.7623286
X-RAY DIFFRACTIONr_scangle_it4.4394.5296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8460.466310.34447066175.794
1.846-1.8970.404270.29753763688.679
1.897-1.9510.334290.24255161794.003
1.951-2.010.316350.24458162299.035
2.01-2.0760.269300.21555358499.829
2.076-2.1480.249240.205573597100
2.148-2.2280.181230.189506529100
2.228-2.3170.218260.192527553100
2.317-2.4190.258190.204512531100
2.419-2.5350.237270.213463490100
2.535-2.670.285200.207459479100
2.67-2.8290.343200.226438458100
2.829-3.020.299300.233416446100
3.02-3.2550.309250.23372397100
3.255-3.5570.328140.208378392100
3.557-3.9610.252140.198341355100
3.961-4.5430.15110.195317328100
4.543-5.4940.195130.221256269100
5.494-7.4890.45580.284232240100
7.489-19.9050.31370.29216517399.422

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