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- PDB-3l0y: Crystal structure OF SCP1 phosphatase D98A mutant -

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Basic information

Entry
Database: PDB / ID: 3l0y
TitleCrystal structure OF SCP1 phosphatase D98A mutant
ComponentsCarboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
KeywordsHYDROLASE / HAD superfamily / Small C-terminal Domain Phosphatase / protein phosphatase
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, M. / Zhang, Y.
CitationJournal: Protein Sci. / Year: 2010
Title: Structural and functional analysis of the phosphoryl transfer reaction mediated by the human small C-terminal domain phosphatase, Scp1.
Authors: Zhang, M. / Liu, J. / Kim, Y. / Dixon, J.E. / Pfaff, S.L. / Gill, G.N. / Noel, J.P. / Zhang, Y.
History
DepositionDec 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
B: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1184
Polymers42,0702
Non-polymers492
Water2,882160
1
A: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0592
Polymers21,0351
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0592
Polymers21,0351
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.791, 78.979, 62.939
Angle α, β, γ (deg.)90.00, 112.79, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-342-

HOH

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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 / NLI-IF


Mass: 21034.912 Da / Num. of mol.: 2 / Fragment: UNP residues 77-256 / Mutation: D98A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTDSP1, NIF3, NLIIF, SCP1 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9GZU7, protein-serine/threonine phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.5M ammonium sulfate, 0.2M lithium sulfate, 100MM HEPES 7.0. Crystal is then transferred to 100MM sodium citrate PH 5.5, 30% PEG8000, 20MM PNPP, 10MM magnesium chloride, VAPOR DIFFUSION, ...Details: 0.5M ammonium sulfate, 0.2M lithium sulfate, 100MM HEPES 7.0. Crystal is then transferred to 100MM sodium citrate PH 5.5, 30% PEG8000, 20MM PNPP, 10MM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2006 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→65.09 Å / Num. obs: 22230 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.072 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.205 / % possible all: 57.2

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GHQ

2ghq


Resolution: 2.3→48.98 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.817 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1131 5.1 %RANDOM
Rwork0.192 ---
obs0.194 22230 89.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å21.28 Å2
2--1.23 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 2 160 3064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222976
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9584048
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.025356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87623.421152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26915486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2511524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022304
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21190
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21962
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2204
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0450.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6721.51829
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20322920
X-RAY DIFFRACTIONr_scbond_it1.76331267
X-RAY DIFFRACTIONr_scangle_it2.8374.51128
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 54 -
Rwork0.24 880 -
obs--51.69 %

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