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- PDB-4ygy: Crystal Structure of Human Scp1 bound to trans-proline peptidomim... -

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Basic information

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


RNA polymerase II CTD heptapeptide repeat phosphatase activity / protein-serine/threonine phosphatase / negative regulation of neuron differentiation / negative regulation of G1/S transition of mitotic cell cycle / protein dephosphorylation / 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 ...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: 2.36 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 1.1Sep 23, 2015Group: Derived calculations
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: peptidomimetic CTD phospho-Ser5 peptide
D: peptidomimetic CTD phospho-Ser5 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7146
Polymers45,6654
Non-polymers492
Water1,11762
1
A: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
C: peptidomimetic CTD phospho-Ser5 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8573
Polymers22,8332
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
D: peptidomimetic CTD phospho-Ser5 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8573
Polymers22,8332
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
C: peptidomimetic CTD phospho-Ser5 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8573
Polymers22,8332
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-13 kcal/mol
Surface area9210 Å2
MethodPISA
4
B: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
D: peptidomimetic CTD phospho-Ser5 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8573
Polymers22,8332
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-14 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.280, 78.335, 63.031
Angle α, β, γ (deg.)90.000, 112.590, 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 peptidomimetic CTD phospho-Ser5 peptide


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


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.38 Å3/Da / Density % sol: 63.6 %
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: APS / Beamline: 23-ID-B / Wavelength: 1.03334 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03334 Å / Relative weight: 1
ReflectionResolution: 2.36→64.86 Å / Num. obs: 22534 / % possible obs: 96.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Χ2: 1.354 / Net I/av σ(I): 29.256 / Net I/σ(I): 15.3 / Num. measured all: 84442
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.36-2.43.10.319581.24285.2
2.4-2.443.20.2510341.23188.5
2.44-2.493.30.23110551.26191.7
2.49-2.543.50.23111201.26795.8
2.54-2.63.70.23611181.27697.2
2.6-2.663.80.19811341.33397.4
2.66-2.723.90.17311331.25698
2.72-2.83.90.14511291.25198.1
2.8-2.883.90.12811421.298.4
2.88-2.973.90.10911511.23198.5
2.97-3.083.90.08111421.25598.5
3.08-3.23.90.0711541.3498.4
3.2-3.353.90.05711351.37398.6
3.35-3.533.90.04811511.42798.9
3.53-3.753.90.0411441.36798.8
3.75-4.033.90.03611581.47298.8
4.03-4.443.90.03311581.66199
4.44-5.083.90.03211451.5798.9
5.08-6.43.80.0311761.45599.2
6.4-503.70.02611971.47899.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→64.86 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.926 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 1105 4.9 %RANDOM
Rwork0.1832 ---
obs0.1862 21427 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.16 Å2 / Biso mean: 47.118 Å2 / Biso min: 27.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å21.81 Å2
2--0.95 Å20 Å2
3----1.39 Å2
Refinement stepCycle: final / Resolution: 2.36→64.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 2 62 3044
Biso mean--53.54 50.27 -
Num. residues----366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193054
X-RAY DIFFRACTIONr_bond_other_d0.0010.022886
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.974156
X-RAY DIFFRACTIONr_angle_other_deg0.86236622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9985360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46823.506154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22415492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3891524
X-RAY DIFFRACTIONr_chiral_restr0.0960.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213404
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02724
X-RAY DIFFRACTIONr_mcbond_it3.7614.431458
X-RAY DIFFRACTIONr_mcbond_other3.7614.431458
X-RAY DIFFRACTIONr_mcangle_it5.2026.6241814
LS refinement shellResolution: 2.359→2.421 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 74 -
Rwork0.257 1384 -
all-1458 -
obs--85.21 %

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