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- PDB-1yo5: Analysis of the 2.0A crystal structure of the protein-DNA complex... -

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Basic information

Entry
Database: PDB / ID: 1yo5
TitleAnalysis of the 2.0A crystal structure of the protein-DNA complex of human PDEF Ets domain bound to the prostate specific antigen regulatory site
Components
  • (Enhancer site of Prostate Specific Antigen Promoter Region) x 2
  • SAM pointed domain containing ets transcription factor
KeywordsTRANSCRIPTION/DNA / ETS / PROTEIN-DNA Complex / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of cell fate commitment / negative regulation of cell fate commitment / lung goblet cell differentiation / epithelial cell fate commitment / glandular epithelial cell development / intestinal epithelial cell development / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific ...positive regulation of cell fate commitment / negative regulation of cell fate commitment / lung goblet cell differentiation / epithelial cell fate commitment / glandular epithelial cell development / intestinal epithelial cell development / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. ...SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / SAM pointed domain-containing Ets transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, Y. / Feng, L. / Said, M. / Balderman, S. / Fayazi, Z. / Liu, Y. / Ghosh, D. / Gulick, A.M.
CitationJournal: Biochemistry / Year: 2005
Title: Analysis of the 2.0 A Crystal Structure of the Protein-DNA Complex of the Human PDEF Ets Domain Bound to the Prostate Specific Antigen Regulatory Site
Authors: Wang, Y. / Feng, L. / Said, M. / Balderman, S. / Fayazi, Z. / Liu, Y. / Ghosh, D. / Gulick, A.M.
History
DepositionJan 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enhancer site of Prostate Specific Antigen Promoter Region
B: Enhancer site of Prostate Specific Antigen Promoter Region
C: SAM pointed domain containing ets transcription factor


Theoretical massNumber of molelcules
Total (without water)19,5303
Polymers19,5303
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.160, 71.476, 39.136
Angle α, β, γ (deg.)90.00, 113.45, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: DNA chain Enhancer site of Prostate Specific Antigen Promoter Region


Mass: 4046.645 Da / Num. of mol.: 1 / Fragment: Sense Strand of E site / Source method: obtained synthetically
Details: This sequence occurs naturally in humans. DNA substrate for protein is synthesized chemically and purified through chromatography
#2: DNA chain Enhancer site of Prostate Specific Antigen Promoter Region


Mass: 3895.563 Da / Num. of mol.: 1 / Fragment: Antisense Strand of E site / Source method: obtained synthetically
Details: This sequence occurs naturally in humans. DNA substrate for protein is synthesized chemically and purified through chromatography
#3: Protein SAM pointed domain containing ets transcription factor


Mass: 11587.606 Da / Num. of mol.: 1 / Fragment: PDEF C-terminal Ets domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDEF / Plasmid: PET-GST-T-A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (Lambda DE3) / References: UniProt: O95238
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2CitrateCitric acid11
3PEG 400012
4Citrate,Citric acid12

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 9, 2004 / Details: Osmic Max-FLUX confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→35.9 Å / Num. all: 11755 / Num. obs: 11176 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.74 % / Biso Wilson estimate: 25.73 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 6.6 / % possible all: 85.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DUX

1dux


Resolution: 2→35.9 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.742 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23889 561 4.8 %RANDOM
Rwork0.20321 ---
obs0.2049 11799 94.72 %-
all-11799 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.592 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å2-0.96 Å2
2---2.84 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 527 0 156 1442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221371
X-RAY DIFFRACTIONr_angle_refined_deg1.3142.4371956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.223587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84121.31638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29315151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.731159
X-RAY DIFFRACTIONr_chiral_restr0.0640.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02851
X-RAY DIFFRACTIONr_nbd_refined0.1810.2539
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2158
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.24
X-RAY DIFFRACTIONr_mcbond_it0.6041.5459
X-RAY DIFFRACTIONr_mcangle_it1.0522712
X-RAY DIFFRACTIONr_scbond_it1.1531218
X-RAY DIFFRACTIONr_scangle_it1.8174.51244
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 39 -
Rwork0.251 726 -
obs--84.72 %

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