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- PDB-3nzl: Crystal Structure of the N-terminal domain of DNA-binding protein... -

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Basic information

Entry
Database: PDB / ID: 3nzl
TitleCrystal Structure of the N-terminal domain of DNA-binding protein SATB1 from Homo sapiens, Northeast Structural Genomics Consortium Target HR4435B
ComponentsDNA-binding protein SATB1
KeywordsTRANSCRIPTION / alpha-helical domain / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / SUMOylation of chromatin organization proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / chromatin organization / double-stranded DNA binding / sequence-specific DNA binding / nuclear body ...Apoptotic cleavage of cellular proteins / SUMOylation of chromatin organization proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / chromatin organization / double-stranded DNA binding / sequence-specific DNA binding / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
SATB, CULT domain / Ubiquitin-like (ULD) domain profile. / CUT repeat-like (CUTL) domain profile. / SATB, CUT1-like DNA-binding domain / SATB, ubiquitin-like oligomerisation domain / SATB, CUTL domain superfamily / SATB, ULD domain superfamily / DNA-binding protein SATB1/SATB2 / Ubiquitin-like oligomerisation domain of SATB / CUT1-like DNA-binding domain of SATB ...SATB, CULT domain / Ubiquitin-like (ULD) domain profile. / CUT repeat-like (CUTL) domain profile. / SATB, CUT1-like DNA-binding domain / SATB, ubiquitin-like oligomerisation domain / SATB, CUTL domain superfamily / SATB, ULD domain superfamily / DNA-binding protein SATB1/SATB2 / Ubiquitin-like oligomerisation domain of SATB / CUT1-like DNA-binding domain of SATB / CUT domain / CUT domain / CUT domain profile. / CUT / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-binding protein SATB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.199 Å
AuthorsForouhar, F. / Abashidze, M. / Seetharaman, J. / Kuzin, A.P. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. ...Forouhar, F. / Abashidze, M. / Seetharaman, J. / Kuzin, A.P. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the N-terminal domain of DNA-binding protein SATB1 from Homo sapiens, Northeast Structural Genomics Consortium Target HR4435B (CASP Target)
Authors: Forouhar, F. / Abashidze, M. / Seetharaman, J. / Kuzin, A.P. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJul 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding protein SATB1


Theoretical massNumber of molelcules
Total (without water)9,9801
Polymers9,9801
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.926, 43.480, 42.461
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA-binding protein SATB1 / Special AT-rich sequence-binding protein 1


Mass: 9980.498 Da / Num. of mol.: 1 / Fragment: Sequence database residues 179-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SATB1 / Plasmid: pET 14-15C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q01826
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.57 Å3/Da / Density % sol: 21.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1M Tris (pH 7.5) and 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97908
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2010 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.199→30 Å / Num. obs: 23439 / % possible obs: 78.3 % / Observed criterion σ(I): 4 / Redundancy: 4.5 % / Biso Wilson estimate: 8.04 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.038 / Net I/σ(I): 35.5
Reflection shellResolution: 1.199→1.35 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 14.7 / Rsym value: 0.09 / % possible all: 59.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SHELXFOLLOWED BY SOLVE/RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.199→22.631 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.09 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Phase error: 14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.177 3552 9.89 %
Rwork0.1477 --
obs0.1505 19319 94.39 %
all-29858 -
Solvent computationShrinkage radii: 0.17 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.311 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2735 Å20 Å2-0 Å2
2--0.0991 Å20 Å2
3----0.3727 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.06 Å
Refinement stepCycle: LAST / Resolution: 1.199→22.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms591 0 0 146 737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01607
X-RAY DIFFRACTIONf_angle_d1.219819
X-RAY DIFFRACTIONf_dihedral_angle_d11.258223
X-RAY DIFFRACTIONf_chiral_restr0.0787
X-RAY DIFFRACTIONf_plane_restr0.01102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1992-1.21570.171460.13831270X-RAY DIFFRACTION92
1.2157-1.2330.20571320.15251217X-RAY DIFFRACTION90
1.233-1.25140.1721510.14371307X-RAY DIFFRACTION94
1.2514-1.2710.2561210.14381233X-RAY DIFFRACTION92
1.271-1.29180.16221350.13831299X-RAY DIFFRACTION93
1.2918-1.31410.18731450.14551264X-RAY DIFFRACTION92
1.3141-1.3380.18711390.12991310X-RAY DIFFRACTION97
1.338-1.36370.15331530.1281326X-RAY DIFFRACTION95
1.3637-1.39150.13891320.12511284X-RAY DIFFRACTION96
1.3915-1.42180.16521560.12931351X-RAY DIFFRACTION97
1.4218-1.45490.15141390.11891317X-RAY DIFFRACTION96
1.4549-1.49120.16051510.12891305X-RAY DIFFRACTION96
1.4912-1.53160.15321330.13131332X-RAY DIFFRACTION97
1.5316-1.57660.151520.11551335X-RAY DIFFRACTION97
1.5766-1.62750.17321540.12331332X-RAY DIFFRACTION98
1.6275-1.68560.15281510.1271336X-RAY DIFFRACTION98
1.6856-1.75310.16941540.13421342X-RAY DIFFRACTION98
1.7531-1.83290.15471420.14011346X-RAY DIFFRACTION98
1.8329-1.92940.18741490.14791316X-RAY DIFFRACTION98
1.9294-2.05030.15961510.13581315X-RAY DIFFRACTION96
2.0503-2.20840.1711350.13311327X-RAY DIFFRACTION97
2.2084-2.43040.21641390.15821294X-RAY DIFFRACTION94
2.4304-2.78160.16381370.15821313X-RAY DIFFRACTION95
2.7816-3.50240.1961370.16071263X-RAY DIFFRACTION92
3.5024-22.63540.19931180.20911024X-RAY DIFFRACTION75

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