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- PDB-4ond: Ancestral Steroid Receptor 2 DBD helix mutant - ERE DNA complex -

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Basic information

Entry
Database: PDB / ID: 4ond
TitleAncestral Steroid Receptor 2 DBD helix mutant - ERE DNA complex
Components
  • 5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*GP*AP*GP*TP*GP*AP*CP*CP*TP*G)-3'
  • 5'-D(*TP*CP*AP*GP*GP*TP*CP*AP*CP*TP*CP*TP*GP*AP*CP*CP*TP*G)-3'
  • Ancestral SR2 Helix Mutant
KeywordsTRANSCRIPTION/DNA / nuclear receptor DNA binding domain / zinc finger / transcription factor / coregulators / TRANSCRIPTION-DNA complex
Function / homologyErythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 2-Layer Sandwich / Alpha Beta / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.253 Å
AuthorsOrtlund, E.O. / Murphy, M.N.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module.
Authors: McKeown, A.N. / Bridgham, J.T. / Anderson, D.W. / Murphy, M.N. / Ortlund, E.A. / Thornton, J.W.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 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_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_auth_seq_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_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_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: Ancestral SR2 Helix Mutant
B: Ancestral SR2 Helix Mutant
E: Ancestral SR2 Helix Mutant
F: Ancestral SR2 Helix Mutant
I: 5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*GP*AP*GP*TP*GP*AP*CP*CP*TP*G)-3'
J: 5'-D(*TP*CP*AP*GP*GP*TP*CP*AP*CP*TP*CP*TP*GP*AP*CP*CP*TP*G)-3'
K: 5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*GP*AP*GP*TP*GP*AP*CP*CP*TP*G)-3'
L: 5'-D(*TP*CP*AP*GP*GP*TP*CP*AP*CP*TP*CP*TP*GP*AP*CP*CP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,74516
Polymers58,2218
Non-polymers5238
Water2,378132
1
A: Ancestral SR2 Helix Mutant
B: Ancestral SR2 Helix Mutant
I: 5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*GP*AP*GP*TP*GP*AP*CP*CP*TP*G)-3'
J: 5'-D(*TP*CP*AP*GP*GP*TP*CP*AP*CP*TP*CP*TP*GP*AP*CP*CP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3728
Polymers29,1114
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-36 kcal/mol
Surface area12560 Å2
MethodPISA
2
E: Ancestral SR2 Helix Mutant
F: Ancestral SR2 Helix Mutant
K: 5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*GP*AP*GP*TP*GP*AP*CP*CP*TP*G)-3'
L: 5'-D(*TP*CP*AP*GP*GP*TP*CP*AP*CP*TP*CP*TP*GP*AP*CP*CP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3728
Polymers29,1114
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-34 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.272, 79.829, 116.782
Angle α, β, γ (deg.)90.000, 96.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ancestral SR2 Helix Mutant


Mass: 9050.774 Da / Num. of mol.: 4 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Details: phylogenetically reconstructed / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: DNA chain 5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*GP*AP*GP*TP*GP*AP*CP*CP*TP*G)-3'


Mass: 5541.592 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: estrogen response element
#3: DNA chain 5'-D(*TP*CP*AP*GP*GP*TP*CP*AP*CP*TP*CP*TP*GP*AP*CP*CP*TP*G)-3'


Mass: 5467.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: estrogen response element
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.84 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG3350, 50 mM ammonium acetate, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2012
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 42779 / Num. obs: 41533 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 45.81 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.24 / Net I/σ(I): 17.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.333.50.78641571.4541100
2.33-2.423.60.45141511.1981100
2.42-2.533.70.3641421.2641100
2.53-2.673.80.27841581.1141100
2.67-2.833.80.19741471.1371100
2.83-3.053.80.12741241.0071100
3.05-3.363.80.0841430.927199.6
3.36-3.853.80.06841581.044199.9
3.85-4.853.80.06642111.368199.9
4.85-503.60.10341421.976197.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_1593refinement
PDB_EXTRACT3.14data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.253→37.563 Å / FOM work R set: 0.8247 / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 1990 4.81 %
Rwork0.1863 --
obs0.1877 41370 98.87 %
all-42779 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.02 Å2 / Biso mean: 55.43 Å2 / Biso min: 26.43 Å2
Refinement stepCycle: LAST / Resolution: 2.253→37.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 1456 8 132 3763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043830
X-RAY DIFFRACTIONf_angle_d0.6685437
X-RAY DIFFRACTIONf_chiral_restr0.029600
X-RAY DIFFRACTIONf_plane_restr0.003454
X-RAY DIFFRACTIONf_dihedral_angle_d22.4981549
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.253-2.30890.3561320.29742636276892
2.3089-2.37130.26651430.249428132956100
2.3713-2.44110.29231440.238828372981100
2.4411-2.51990.26521440.231528322976100
2.5199-2.60990.27791410.239527882929100
2.6099-2.71440.29631430.233428472990100
2.7144-2.83790.27671450.231928432988100
2.8379-2.98740.29661430.225828202963100
2.9874-3.17450.24891410.218228132954100
3.1745-3.41940.22271380.18772790292898
3.4194-3.76330.21031430.17442828297199
3.7633-4.30720.19041450.151628442989100
4.3072-5.42390.17181450.1528673012100
5.4239-37.56850.16061430.16322822296597
Refinement TLS params.Method: refined / Origin x: -9.802 Å / Origin y: 11.877 Å / Origin z: -29.3716 Å
111213212223313233
T0.3283 Å2-0.0618 Å20.0093 Å2-0.3381 Å20.0076 Å2--0.3029 Å2
L1.0412 °2-0.2238 °20.5469 °2-0.4166 °2-0.2817 °2--1.6048 °2
S0.021 Å °-0.0809 Å °0.0301 Å °0.0542 Å °-0.0043 Å °-0.0654 Å °-0.033 Å °0.0343 Å °-0.0177 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 241
2X-RAY DIFFRACTION1allI101
3X-RAY DIFFRACTION1allB5 - 231
4X-RAY DIFFRACTION1allE4 - 224
5X-RAY DIFFRACTION1allF4 - 236

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