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- PDB-3l0b: Crystal structure of SCP1 phosphatase D206A mutant phosphoryl-int... -

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Basic information

Entry
Database: PDB / ID: 3l0b
TitleCrystal structure of SCP1 phosphatase D206A mutant phosphoryl-intermediate
ComponentsCarboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
KeywordsHYDROLASE / HAD superfamily / phosphoryl-aspartate intermediate / small C-terminal domain phosphatase / protein phosphatase
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat phosphatase activity / negative regulation of neuron differentiation / protein-serine/threonine phosphatase / 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
Chem-1PG / 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: 2.35 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 9, 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_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_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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)42,5064
Polymers42,2302
Non-polymers2772
Water1,72996
1
A: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3923
Polymers21,1151
Non-polymers2772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1


Theoretical massNumber of molelcules
Total (without water)21,1151
Polymers21,1151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.666, 78.187, 62.585
Angle α, β, γ (deg.)90.00, 112.34, 90.00
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 / NLI-IF


Mass: 21114.893 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN / Mutation: D206A
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.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5M AMMONIUM SULFATE, 0.2M LITHIUM SULFATE, 100MM HEPES, PH 7.0. CRYSTAL TRANSFERRED TO 100MM SODIUM CITRATE, PH 5.5, 30% PEG8000, 20MM PNPP, and 10mM Magnesium chloride, VAPOR DIFFUSION, ...Details: 0.5M AMMONIUM SULFATE, 0.2M LITHIUM SULFATE, 100MM HEPES, PH 7.0. CRYSTAL TRANSFERRED TO 100MM SODIUM CITRATE, PH 5.5, 30% PEG8000, 20MM PNPP, and 10mM Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: 2.35→64.7 Å / Num. obs: 21278 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.071 / Net I/σ(I): 16
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.204 / % possible all: 59.1

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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: pdb entry 2GHQ

2ghq


Resolution: 2.35→64.68 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.685 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24947 1109 5.2 %RANDOM
Rwork0.18997 ---
obs0.19299 20222 91.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.431 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20.94 Å2
2--1.14 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.35→64.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 18 96 3040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223014
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.9644094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8725358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37623.464153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.72915489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4581524
X-RAY DIFFRACTIONr_chiral_restr0.1250.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212320
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21253
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21997
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2160
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2360.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0371.51808
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96222936
X-RAY DIFFRACTIONr_scbond_it3.04331206
X-RAY DIFFRACTIONr_scangle_it4.7794.51158
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.407 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 56 -
Rwork0.259 951 -
obs--58.44 %

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