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- PDB-4oor: Ancestral Steroid Receptor 2 DNA binding domain in complex with a... -

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Basic information

Entry
Database: PDB / ID: 4oor
TitleAncestral Steroid Receptor 2 DNA binding domain in complex with a steroid response element
Components
  • 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3'
  • 5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3'
  • Ancestral Steroid Receptor 2 DNA binding domain
KeywordsTRANSCRIPTION/DNA / nuclear receptor zinc finger / steroid receptor / transcription factor / DNA / 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 / Resolution: 2.701 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
DepositionFeb 3, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 Steroid Receptor 2 DNA binding domain
B: Ancestral Steroid Receptor 2 DNA binding domain
E: Ancestral Steroid Receptor 2 DNA binding domain
F: Ancestral Steroid Receptor 2 DNA binding domain
I: 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3'
J: 5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3'
K: 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3'
L: 5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,68516
Polymers58,1618
Non-polymers5238
Water95553
1
A: Ancestral Steroid Receptor 2 DNA binding domain
B: Ancestral Steroid Receptor 2 DNA binding domain
I: 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3'
J: 5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3428
Polymers29,0814
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-33 kcal/mol
Surface area12410 Å2
MethodPISA
2
E: Ancestral Steroid Receptor 2 DNA binding domain
F: Ancestral Steroid Receptor 2 DNA binding domain
K: 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3'
L: 5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3428
Polymers29,0814
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-31 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.472, 80.374, 115.645
Angle α, β, γ (deg.)90.000, 96.740, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
31chain E and segid E
41chain F and segid F
12chain I and segid I
22chain J and segid J
32chain K and segid K
42chain L and segid L

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
311chain E and segid EE0
411chain F and segid FF0
112chain I and segid II0
212chain J and segid JJ0
312chain K and segid KK0
412chain L and segid LL0

NCS ensembles :
ID
1
2

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Components

#1: Protein
Ancestral Steroid Receptor 2 DNA binding domain


Mass: 9036.792 Da / Num. of mol.: 4
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*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3'


Mass: 5540.604 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: steroid response element DNA
#3: DNA chain 5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3'


Mass: 5466.553 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: steroid response element DNA
#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.: 53 / 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: 3.77 Å3/Da / Density % sol: 67.35 %
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: Apr 23, 2011
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: 2.7→40 Å / Num. obs: 23370 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 44.54 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.857 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.762.50.35613251.175182.3
2.76-2.832.70.29814431.096191.7
2.83-2.9130.31215051.135196.7
2.91-2.993.30.29916081.06199.5
2.99-3.093.50.24715401.14199.8
3.09-3.23.60.15615951.168199.9
3.2-3.333.70.0815871.3361100
3.33-3.483.70.10915712.3511100
3.48-3.663.70.10315901.8061100
3.66-3.893.70.08915972.103199.9
3.89-4.193.70.06815681.987199.9
4.19-4.623.70.06215972.0581100
4.62-5.283.70.05916061.9571100
5.28-6.653.70.05316092.512199.9
6.65-403.60.04316293.863199.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_1593refinement
PDB_EXTRACT3.14data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.701→30.583 Å / FOM work R set: 0.801 / SU ML: 0.34 / σ(F): 1.35 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 1191 5.12 %RANDOM
Rwork0.1905 ---
obs0.1926 23265 97.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.9 Å2 / Biso mean: 51.07 Å2 / Biso min: 13.01 Å2
Refinement stepCycle: LAST / Resolution: 2.701→30.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 1460 8 53 3685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043823
X-RAY DIFFRACTIONf_angle_d0.7665430
X-RAY DIFFRACTIONf_chiral_restr0.033604
X-RAY DIFFRACTIONf_plane_restr0.003446
X-RAY DIFFRACTIONf_dihedral_angle_d23.1661540
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1309X-RAY DIFFRACTION5.895TORSIONAL
12B1309X-RAY DIFFRACTION5.895TORSIONAL
13E1309X-RAY DIFFRACTION5.895TORSIONAL
14F1309X-RAY DIFFRACTION5.895TORSIONAL
21I704X-RAY DIFFRACTION5.895TORSIONAL
22J704X-RAY DIFFRACTION5.895TORSIONAL
23K704X-RAY DIFFRACTION5.895TORSIONAL
24L704X-RAY DIFFRACTION5.895TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.701-2.80940.36041040.2752141224585
2.8094-2.93720.33031260.27482407253396
2.9372-3.09190.35421340.267424812615100
3.0919-3.28540.25251400.23922469260999
3.2854-3.53870.26731260.20572463258999
3.5387-3.89420.21891440.188725272671100
3.8942-4.45620.2061540.15824812635100
4.4562-5.60870.21271340.157125272661100
5.6087-30.58520.16681290.153825782707100
Refinement TLS params.Method: refined / Origin x: -7.3274 Å / Origin y: -27.7265 Å / Origin z: -28.3076 Å
111213212223313233
T0.1741 Å20.0754 Å20.0054 Å2-0.1295 Å20.002 Å2--0.1654 Å2
L1.1593 °20.2743 °20.4596 °2-0.4616 °20.3151 °2--1.2542 °2
S0.0409 Å °-0.0065 Å °-0.0278 Å °0.0014 Å °0.0041 Å °-0.0443 Å °-0.0085 Å °0.0015 Å °0.0022 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 207
2X-RAY DIFFRACTION1allB5 - 209
3X-RAY DIFFRACTION1allE3 - 205
4X-RAY DIFFRACTION1allF4 - 216
5X-RAY DIFFRACTION1allI1 - 103
6X-RAY DIFFRACTION1allK1 - 106
7X-RAY DIFFRACTION1allJ1 - 102
8X-RAY DIFFRACTION1allL1 - 105

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