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- PDB-4iuq: crystal structure of SHH1 SAWADEE domain -

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Basic information

Entry
Database: PDB / ID: 4iuq
Titlecrystal structure of SHH1 SAWADEE domain
ComponentsSAWADEE HOMEODOMAIN HOMOLOG 1
KeywordsGENE REGULATION / tandem tudor / zinc finger / mediate interaction / histone
Function / homology
Function and homology information


: / DNA methylation-dependent heterochromatin formation / regulatory ncRNA-mediated gene silencing / chromatin binding / metal ion binding / nucleus
Similarity search - Function
SAWADEE domain / Protein SAWADEE HOMEODOMAIN HOMOLOG 1/2 / SAWADEE domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / SH3 type barrels. - #140 / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CYMAL-4 / Protein SAWADEE HOMEODOMAIN HOMOLOG 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.809 Å
AuthorsDu, J. / Patel, D.J.
CitationJournal: Nature / Year: 2013
Title: Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.
Authors: Law, J.A. / Du, J. / Hale, C.J. / Feng, S. / Krajewski, K. / Palanca, A.M. / Strahl, B.D. / Patel, D.J. / Jacobsen, S.E.
History
DepositionJan 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_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
B: SAWADEE HOMEODOMAIN HOMOLOG 1
A: SAWADEE HOMEODOMAIN HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6536
Polymers31,5612
Non-polymers1,0924
Water0
1
B: SAWADEE HOMEODOMAIN HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3273
Polymers15,7811
Non-polymers5462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: SAWADEE HOMEODOMAIN HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3273
Polymers15,7811
Non-polymers5462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.708, 117.691, 53.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SAWADEE HOMEODOMAIN HOMOLOG 1 / Uncharacterized protein


Mass: 15780.645 Da / Num. of mol.: 2 / Fragment: SHH1 SAWADEE domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F9L1.16, At1g15215, AT1G15215 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9XI47
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CVM / CYMAL-4 / 4-CYCLOHEXYLBUTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE


Mass: 480.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H40O11

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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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2819 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2011
RadiationMonochromator: SI MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2819 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 16108 / Num. obs: 16076 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 14.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1593 / Rsym value: 0.412 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IUP

4iup


Resolution: 2.809→40.067 Å / SU ML: 0.45 / σ(F): 0.97 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 420 4.87 %RANDOM
Rwork0.2008 ---
obs0.2038 16030 98.74 %-
all-16810 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.237 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.1694 Å20 Å20 Å2
2---0.7714 Å20 Å2
3----5.398 Å2
Refinement stepCycle: LAST / Resolution: 2.809→40.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 68 0 2220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192262
X-RAY DIFFRACTIONf_angle_d1.6923055
X-RAY DIFFRACTIONf_dihedral_angle_d17.566876
X-RAY DIFFRACTIONf_chiral_restr0.102339
X-RAY DIFFRACTIONf_plane_restr0.006392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8093-2.98530.35921320.29332393X-RAY DIFFRACTION94
2.9853-3.21570.33271480.23482562X-RAY DIFFRACTION100
3.2157-3.53910.221350.21522555X-RAY DIFFRACTION100
3.5391-4.05080.26591110.18732600X-RAY DIFFRACTION100
4.0508-5.10190.24611260.15692570X-RAY DIFFRACTION100
5.1019-40.07140.2341280.20592570X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.30910.0381-0.00450.609-0.01470.0083-0.12810.19390.0573-0.02410.14010.072-0.02580.0881-0.19830.2351-0.12630.02220.32670.12470.129612.352426.33784.5629
20.6109-0.14630.72920.0987-0.34691.3341-0.1143-0.1430.05830.12980.03810.1656-0.0799-0.2914-0.13380.1316-0.03110.06180.1897-0.03310.32134.494720.13068.7257
30.4733-0.0823-0.3650.05110.00440.3353-0.3593-0.1393-0.04110.2814-0.1796-0.05320.16290.28020.00830.27920.0347-0.0080.2366-0.02350.217612.983321.420823.6851
40.30.06650.20510.12180.01840.1595-0.0011-0.02390.00680.121-0.27570.15950.0359-0.34780.03490.0167-0.0141-0.03510.5202-0.0860.20714.906325.70814.1108
50.2520.2375-0.04221.3722-0.170.92150.1170.10530.23810.2368-0.2466-0.28860.07050.11210.03420.1673-0.03430.05160.2911-0.00620.253810.691520.60512.5467
60.5972-0.2577-0.84040.13220.14243.11870.10930.0476-0.0314-0.2634-0.17250.0829-0.2499-0.0668-0.12670.21360.019-0.02050.0790.0810.317710.879623.3377-6.4245
70.64680.4853-0.10080.4069-0.27671.1163-0.22540.2027-0.3015-0.01850.2375-0.20190.42640.33870.13560.34330.1103-0.0110.2526-0.00970.274115.906515.5167-12.6615
80.0029-0.0209-0.03890.24460.3820.5978-0.2209-0.0666-0.06680.3921-0.37050.69430.0968-0.4982-0.56160.0396-0.2922-0.0114-0.165-0.19510.5567-0.114412.4557-2.0338
90.42790.2117-0.30690.8786-0.27691.3911-0.15990.2063-0.3954-0.2665-0.07680.02620.65280.05370.02790.38870.0429-0.01310.17880.00690.2938.238411.5448-11.9841
100.39510.2947-0.17140.216-0.12750.07540.08090.0815-0.4587-0.15190.15410.02460.0612-0.0011-0.08010.6261-0.39590.078-0.0898-0.01790.35885.27575.3369-2.7775
110.1161-0.22010.28910.9141-0.0091.32090.1134-0.08490.0174-0.09550.14240.0204-0.02740.16390.08730.1010.04680.04080.3269-0.00660.196210.990318.1613-6.6562
120.2418-0.1730.21450.67790.10370.46670.0486-0.0713-0.1663-0.06660.1620.0818-0.1436-0.0407-0.01930.20.0204-0.02180.15110.00120.1894-11.139919.361336.8662
130.38740.3211-0.08070.62850.22980.73040.13630.0919-0.06470.5290.1735-0.06440.5753-0.0874-0.00870.2617-0.0362-0.07050.20250.01120.1797-16.739816.338742.3093
140.5643-0.08620.02310.45250.57251.3836-0.13220.26940.2441-0.0504-0.08490.1922-0.40420.0278-0.02260.16210.0221-0.01310.22180.00990.1618-12.624217.449923.0494
150.26830.12670.05770.4656-0.25970.5886-0.2033-0.0324-0.16780.21280.1213-0.2560.85680.33160.10010.55580.0524-0.00150.1801-0.04540.2617-14.69422.985425.657
160.9641-0.0623-0.22770.2257-0.02590.13810.09020.1694-0.0637-0.4197-0.0831-0.00160.4916-0.13080.06640.39620.0201-0.06650.2746-0.02480.2619-15.81717.665812.4101
171.27430.2836-0.07580.7363-0.82571.3105-0.1928-0.1379-0.3218-0.1387-0.3119-0.45920.20310.1547-0.09110.32420.05590.00240.1657-0.09550.2945-7.89353.182819.2829
180.3859-0.29150.06390.4328-0.00220.4550.08620.53710.1503-0.07020.04790.026-0.0833-0.4706-0.00730.2632-0.0243-0.00830.3524-0.0380.2915-15.554514.132818.4283
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 125:132)
2X-RAY DIFFRACTION2chain 'B' and (resseq 133:145)
3X-RAY DIFFRACTION3chain 'B' and (resseq 146:155)
4X-RAY DIFFRACTION4chain 'B' and (resseq 156:169)
5X-RAY DIFFRACTION5chain 'B' and (resseq 170:181)
6X-RAY DIFFRACTION6chain 'B' and (resseq 182:187)
7X-RAY DIFFRACTION7chain 'B' and (resseq 188:198)
8X-RAY DIFFRACTION8chain 'B' and (resseq 199:209)
9X-RAY DIFFRACTION9chain 'B' and (resseq 210:238)
10X-RAY DIFFRACTION10chain 'B' and (resseq 239:248)
11X-RAY DIFFRACTION11chain 'B' and (resseq 249:257)
12X-RAY DIFFRACTION12chain 'A' and (resseq 124:155)
13X-RAY DIFFRACTION13chain 'A' and (resseq 156:170)
14X-RAY DIFFRACTION14chain 'A' and (resseq 171:198)
15X-RAY DIFFRACTION15chain 'A' and (resseq 199:209)
16X-RAY DIFFRACTION16chain 'A' and (resseq 210:232)
17X-RAY DIFFRACTION17chain 'A' and (resseq 233:248)
18X-RAY DIFFRACTION18chain 'A' and (resseq 249:257)

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