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- PDB-7wrn: ESRP1 RNaseH-qRRM1 tandem domain -

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Basic information

Entry
Database: PDB / ID: 7wrn
TitleESRP1 RNaseH-qRRM1 tandem domain
ComponentsEpithelial splicing regulatory protein 1
KeywordsSPLICING / qRRM domain / RNA binding / circRNA / RNA BINDING PROTEIN / RNase-H
Function / homology
Function and homology information


regulation of inner ear auditory receptor cell fate specification / FGFR2 alternative splicing / regulation of RNA splicing / RNA splicing / mRNA processing / Signaling by BRAF and RAF1 fusions / nuclear body / ribonucleoprotein complex / mRNA binding / nucleoplasm / nucleus
Similarity search - Function
ESRP1, RNA recognition motif 1 / : / Ribonuclease H-like superfamily/Ribonuclease H / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily ...ESRP1, RNA recognition motif 1 / : / Ribonuclease H-like superfamily/Ribonuclease H / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Epithelial splicing regulatory protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWu, B.X. / Guo, W.T. / Patel, D.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: ESRP1 RNaseH-qRRM1 tandem domain
Authors: Wu, B.X. / Guo, W.T. / Patel, D.J.
History
DepositionJan 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epithelial splicing regulatory protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8602
Polymers34,7671
Non-polymers921
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint1 kcal/mol
Surface area14910 Å2
Unit cell
Length a, b, c (Å)70.365, 70.365, 114.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein Epithelial splicing regulatory protein 1 / RNA-binding motif protein 35A / RNA-binding protein 35A


Mass: 34767.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESRP1, RBM35A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6NXG1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 25216 / % possible obs: 100 % / Redundancy: 25.4 % / Biso Wilson estimate: 24.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.022 / Rrim(I) all: 0.111 / Net I/σ(I): 26.9
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 25.6 % / Rmerge(I) obs: 1.084 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3581 / CC1/2: 0.894 / Rpim(I) all: 0.217 / Rrim(I) all: 1.106 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VKI

7vki


Resolution: 1.85→29.94 Å / SU ML: 0.1636 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.836
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.231 1239 4.92 %
Rwork0.1935 23926 -
obs0.1954 25165 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.16 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 6 125 2478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812425
X-RAY DIFFRACTIONf_angle_d1.00223274
X-RAY DIFFRACTIONf_chiral_restr0.059359
X-RAY DIFFRACTIONf_plane_restr0.007432
X-RAY DIFFRACTIONf_dihedral_angle_d6.0658329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.24771330.21922586X-RAY DIFFRACTION99.96
1.92-2.010.2781240.21462607X-RAY DIFFRACTION99.93
2.01-2.120.27811290.21122620X-RAY DIFFRACTION99.96
2.12-2.250.2331280.2042622X-RAY DIFFRACTION100
2.25-2.420.26211330.21032640X-RAY DIFFRACTION100
2.42-2.670.27041390.21142638X-RAY DIFFRACTION100
2.67-3.050.23351590.20442650X-RAY DIFFRACTION99.96
3.05-3.840.23151420.17892711X-RAY DIFFRACTION100
3.85-29.940.18771520.17522852X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -7.84778518298 Å / Origin y: -20.9606789864 Å / Origin z: -28.2923155271 Å
111213212223313233
T0.133074669003 Å20.0190556030535 Å20.00824540677842 Å2-0.114055716865 Å20.00632672427415 Å2--0.166879709838 Å2
L1.17267500373 °20.188027376833 °20.532903950126 °2-0.900994143224 °20.235314370548 °2--2.20014565218 °2
S0.0356693999424 Å °0.0114465925935 Å °-0.0182873497467 Å °-0.0429527800432 Å °-0.0240779232151 Å °0.0464394777219 Å °0.0647166976828 Å °0.159663331566 Å °-0.011103371552 Å °
Refinement TLS groupSelection details: all

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