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- PDB-4n1y: Crystal Structure of the Pacific Oyster Estrogen Receptor Ligand ... -

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Basic information

Entry
Database: PDB / ID: 4n1y
TitleCrystal Structure of the Pacific Oyster Estrogen Receptor Ligand Binding Domain
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / estrogen / Nuclear Hormone Receptor / Endocrine signaling
Function / homology
Function and homology information


nuclear steroid receptor activity / steroid binding / sequence-specific DNA binding / DNA-binding transcription factor activity / zinc ion binding / nucleus
Similarity search - Function
Estrogen receptor/oestrogen-related receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain ...Estrogen receptor/oestrogen-related receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCrassostrea gigas (Pacific oyster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.605 Å
AuthorsOrtlund, E.O.
CitationJournal: PLoS Genet / Year: 2014
Title: Vestigialization of an allosteric switch: genetic and structural mechanisms for the evolution of constitutive activity in a steroid hormone receptor.
Authors: Bridgham, J.T. / Keay, J. / Ortlund, E.A. / Thornton, J.W.
History
DepositionOct 4, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 12, 2014ID: 3LTX
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Other
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
C: Estrogen receptor
D: Estrogen receptor


Theoretical massNumber of molelcules
Total (without water)108,5054
Polymers108,5054
Non-polymers00
Water93752
1
A: Estrogen receptor
B: Estrogen receptor


Theoretical massNumber of molelcules
Total (without water)54,2532
Polymers54,2532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-9 kcal/mol
Surface area18790 Å2
MethodPISA
2
C: Estrogen receptor
D: Estrogen receptor


Theoretical massNumber of molelcules
Total (without water)54,2532
Polymers54,2532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-10 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.035, 105.795, 171.503
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Estrogen receptor /


Mass: 27126.266 Da / Num. of mol.: 4 / Fragment: unp residues 245-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crassostrea gigas (Pacific oyster) / Gene: CGI_10024100 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: K1QUU5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 46.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG 4K, 10% glycerol, 0.1M Tris-HCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Feb 8, 2008 / Details: Si 111 CHANNEL
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 28364 / Num. obs: 28364 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.14 / Χ2: 1.545 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.695.20.41619621.493164.1
2.69-2.85.60.39222091.484171.7
2.8-2.9360.35224311.536178.2
2.93-3.086.50.33127201.475187.9
3.08-3.287.20.28830561.5198.1
3.28-3.538.10.21631241.55199.7
3.53-3.888.40.16231411.515199.9
3.88-4.458.50.1231391.623199.9
4.45-5.68.30.132181.4621100
5.6-507.90.09733641.706199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_1458refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.605→46.958 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7961 / SU ML: 0.32 / σ(F): 1.33 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 1409 4.98 %Random
Rwork0.1702 ---
obs0.1738 28311 89.93 %-
all-28364 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.63 Å2 / Biso mean: 54.6555 Å2 / Biso min: 23.75 Å2
Refinement stepCycle: LAST / Resolution: 2.605→46.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7166 0 0 52 7218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097302
X-RAY DIFFRACTIONf_angle_d1.3019915
X-RAY DIFFRACTIONf_chiral_restr0.0521175
X-RAY DIFFRACTIONf_plane_restr0.0061266
X-RAY DIFFRACTIONf_dihedral_angle_d14.8932679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6046-2.69770.3496940.21111780187461
2.6977-2.80570.2921220.21012101222372
2.8057-2.93340.3081110.20432325243679
2.9334-3.0880.26981410.22112603274488
3.088-3.28150.29921330.20512933306698
3.2815-3.53470.27621560.178129663122100
3.5347-3.89030.21021440.166929893133100
3.8903-4.45290.22261650.146429893154100
4.4529-5.60870.23531790.148930273206100
5.6087-46.96570.2061640.157431893353100
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)
12.0870.35141.50421.26510.48661.76610.02250.0099-0.0006-0.12450.0794-0.05950.07070.0009-0.07730.37290.00030.02170.36330.02640.282924.3429-11.32468.0188
22.0327-0.4258-0.64032.7642-0.7973.1788-0.04060.09160.45390.13680.25160.223-0.5174-0.2626-0.21110.38410.00340.02280.32580.05480.414322.194614.317211.1814
32.9422-0.36911.12071.7810.22012.77810.08530.5072-0.1081-0.0386-0.0421-0.2317-0.03650.6164-0.05320.2917-0.04160.00530.64690.05850.347426.0765-4.4163-35.4195
40.42880.38860.12191.9756-1.16692.1296-0.0228-0.08220.08470.09260.0520.1078-0.0387-0.1385-0.01320.2530.03660.01610.45060.02090.31240.7988-6.3192-30.9052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 248:473)A248 - 473
2X-RAY DIFFRACTION2(chain B and resseq 248:474)B248 - 474
3X-RAY DIFFRACTION3(chain C and resseq 249:472)C249 - 472
4X-RAY DIFFRACTION4(chain D and resseq 248:473)D248 - 473

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