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- PDB-4mcf: Crystal structure of the Gas5 GRE Mimic -

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Basic information

Entry
Database: PDB / ID: 4mcf
TitleCrystal structure of the Gas5 GRE Mimic
Components
  • Gas5 GREM Fwd
  • Gas5 GREM Rev
KeywordsRNA / RNA Double Helix
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsHudson, W.H. / Ortlund, E.A.
CitationJournal: Nat Commun / Year: 2014
Title: Conserved sequence-specific lincRNA-steroid receptor interactions drive transcriptional repression and direct cell fate.
Authors: Hudson, W.H. / Pickard, M.R. / de Vera, I.M. / Kuiper, E.G. / Mourtada-Maarabouni, M. / Conn, G.L. / Kojetin, D.J. / Williams, G.T. / Ortlund, E.A.
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Mar 28, 2018Group: Data collection / Derived calculations / Source and taxonomy
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Feb 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_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Gas5 GREM Fwd
D: Gas5 GREM Rev
A: Gas5 GREM Fwd
B: Gas5 GREM Rev
E: Gas5 GREM Fwd
F: Gas5 GREM Rev
G: Gas5 GREM Fwd
H: Gas5 GREM Rev
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,02812
Polymers26,6448
Non-polymers3844
Water46826
1
C: Gas5 GREM Fwd
D: Gas5 GREM Rev


Theoretical massNumber of molelcules
Total (without water)6,6612
Polymers6,6612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-6 kcal/mol
Surface area3990 Å2
MethodPISA
2
A: Gas5 GREM Fwd
B: Gas5 GREM Rev
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9495
Polymers6,6612
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-15 kcal/mol
Surface area3920 Å2
MethodPISA
3
E: Gas5 GREM Fwd
F: Gas5 GREM Rev
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7573
Polymers6,6612
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-8 kcal/mol
Surface area3790 Å2
MethodPISA
4
G: Gas5 GREM Fwd
H: Gas5 GREM Rev


  • defined by author&software
  • 6.66 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)6,6612
Polymers6,6612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-7 kcal/mol
Surface area3810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.314, 43.314, 304.179
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-101-

SO4

21A-101-

SO4

31B-101-

SO4

41B-101-

SO4

51B-102-

SO4

61F-101-

SO4

71F-101-

SO4

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Components

#1: RNA chain
Gas5 GREM Fwd


Mass: 3154.892 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: RNA Synthesis / Source: (synth.) Homo sapiens (human)
#2: RNA chain
Gas5 GREM Rev


Mass: 3506.154 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: RNA Synthesis / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M citric acid pH 4 3 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 23567 / Num. obs: 23520 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.064
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.632 / % possible all: 99.3

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Processing

Software
NameVersionClassification
JDirectordata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.899→22.258 Å / SU ML: 0.26 / σ(F): 1.97 / Phase error: 29.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 1677 10.02 %
Rwork0.2302 --
obs0.2335 16738 99.42 %
all-16836 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5944 Å20 Å2-0 Å2
2--0.5944 Å20 Å2
3----1.1888 Å2
Refinement stepCycle: LAST / Resolution: 1.899→22.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1639 20 26 1685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041839
X-RAY DIFFRACTIONf_angle_d0.9792849
X-RAY DIFFRACTIONf_dihedral_angle_d8.499908
X-RAY DIFFRACTIONf_chiral_restr0.037385
X-RAY DIFFRACTIONf_plane_restr0.00678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8988-1.95460.32821440.24261271X-RAY DIFFRACTION100
1.9546-2.01770.24671350.23271243X-RAY DIFFRACTION100
2.0177-2.08970.26621380.22481285X-RAY DIFFRACTION100
2.0897-2.17330.31951360.22771268X-RAY DIFFRACTION100
2.1733-2.27210.28041390.24151274X-RAY DIFFRACTION100
2.2721-2.39180.31521350.24221246X-RAY DIFFRACTION100
2.3918-2.54150.29761420.27551258X-RAY DIFFRACTION100
2.5415-2.73740.34151430.28481257X-RAY DIFFRACTION100
2.7374-3.01220.33311430.2971251X-RAY DIFFRACTION99
3.0122-3.44670.26881410.23861229X-RAY DIFFRACTION99
3.4467-4.33730.22761420.19241241X-RAY DIFFRACTION97
4.3373-22.25980.18011390.18181238X-RAY DIFFRACTION98

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