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- PDB-4yh1: Structure of Human Scp1 bound to cis-proline peptidomimetic CTD p... -

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Basic information

Entry
Database: PDB / ID: 4yh1
TitleStructure of Human Scp1 bound to cis-proline peptidomimetic CTD phospho-Ser5 peptide
Components
  • A small phosphatase 1
  • Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
KeywordsHYDROLASE / Phosphatase / Peptidomimetic / Complex
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat phosphatase activity / myosin phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / protein-serine/threonine phosphatase / negative regulation of neuron differentiation / protein dephosphorylation / negative regulation of protein phosphorylation / negative regulation of neurogenesis / regulation of transcription by RNA polymerase II / extracellular exosome ...RNA polymerase II CTD heptapeptide repeat phosphatase activity / myosin phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / protein-serine/threonine phosphatase / negative regulation of neuron differentiation / protein dephosphorylation / negative regulation of protein phosphorylation / negative regulation of neurogenesis / regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Dullard phosphatase domain, eukaryotic / CTD small RNA polymerase II polypeptide A phosphatase-like / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold ...Dullard phosphatase domain, eukaryotic / CTD small RNA polymerase II polypeptide A phosphatase-like / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMayfield, J.E. / Zhang, Y.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II.
Authors: Mayfield, J.E. / Fan, S. / Wei, S. / Zhang, M. / Li, B. / Ellington, A.D. / Etzkorn, F.A. / Zhang, Y.J.
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
B: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
C: A small phosphatase 1
D: A small phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7146
Polymers45,6654
Non-polymers492
Water2,540141
1
A: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
C: A small phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8573
Polymers22,8332
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-14 kcal/mol
Surface area9090 Å2
MethodPISA
2
B: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
D: A small phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8573
Polymers22,8332
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-14 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.115, 78.804, 62.853
Angle α, β, γ (deg.)90.000, 112.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 / Nuclear LIM interactor-interacting factor 3 / NLI-interacting factor 3 / Small C-terminal domain ...Nuclear LIM interactor-interacting factor 3 / NLI-interacting factor 3 / Small C-terminal domain phosphatase 1 / Small CTD phosphatase 1


Mass: 21573.492 Da / Num. of mol.: 2 / Fragment: unp residues 76-254 / Mutation: D96N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTDSP1, NIF3, NLIIF, SCP1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9GZU7, protein-serine/threonine phosphatase
#2: Protein/peptide A small phosphatase 1


Mass: 1259.238 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30% PEG 3350, 0.2 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 27838 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Χ2: 0.997 / Net I/av σ(I): 11.25 / Net I/σ(I): 6.3 / Num. measured all: 101636
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.242.80.49512000.70883
2.24-2.282.90.47412320.71687.7
2.28-2.323.10.47313520.73593.3
2.32-2.373.40.49413530.71595.9
2.37-2.423.60.44314110.68798.1
2.42-2.483.80.38513900.72397.9
2.48-2.543.80.37614060.76898.4
2.54-2.613.80.35513930.77898.3
2.61-2.693.80.29513960.82298.4
2.69-2.773.80.24414110.85298.5
2.77-2.873.80.21514280.90798.7
2.87-2.993.80.18113990.95898.7
2.99-3.123.80.14114041.06498.8
3.12-3.293.80.11314321.12698.8
3.29-3.493.80.09514361.38499
3.49-3.763.80.07914051.37299.1
3.76-4.143.80.06614411.63199.2
4.14-4.743.70.05414171.45299.3
4.74-5.973.60.04514431.10899.5
5.97-503.80.03314891.03699.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.808 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 1469 5.3 %RANDOM
Rwork0.1925 26369 --
obs0.1953 26369 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.04 Å2 / Biso mean: 33.578 Å2 / Biso min: 11.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20.67 Å2
2--1.67 Å20 Å2
3----1.38 Å2
Refinement stepCycle: final / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 2 141 3123
Biso mean--53.61 37.96 -
Num. residues----366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193054
X-RAY DIFFRACTIONr_bond_other_d0.0010.022890
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.974156
X-RAY DIFFRACTIONr_angle_other_deg0.88436632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7425360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9523.506154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16815492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0651524
X-RAY DIFFRACTIONr_chiral_restr0.1010.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213426
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02732
X-RAY DIFFRACTIONr_mcbond_it2.5673.1141458
X-RAY DIFFRACTIONr_mcbond_other2.5613.1141458
X-RAY DIFFRACTIONr_mcangle_it3.7814.6421814
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 103 -
Rwork0.306 1644 -
all-1747 -
obs--83.15 %

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