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- PDB-1t9z: Three-dimensional structure of a RNA-polymerase II binding protein. -

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Basic information

Entry
Database: PDB / ID: 1t9z
TitleThree-dimensional structure of a RNA-polymerase II binding protein.
ComponentsCarboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
KeywordsHYDROLASE / alpha-beta protein
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 / nucleus / metal ion binding
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
CITRIC ACID / Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsKamenski, T. / Heilmeier, S. / Meinhart, A. / Cramer, P.
CitationJournal: Mol.Cell / Year: 2004
Title: Structure and Mechanism of RNA Polymerase II CTD Phosphatases.
Authors: Kamenski, T. / Heilmeier, S. / Meinhart, A. / Cramer, P.
History
DepositionMay 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1383
Polymers22,9211
Non-polymers2162
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.550, 47.190, 39.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 / Scp1


Mass: 22921.283 Da / Num. of mol.: 1 / Mutation: L165M, L205M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTDSP1, NIF3, NLIIF / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1.3 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 3300, ammonium acetate, citrate buffer, DTT , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795, 0.9797, 0.9686
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 3, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.96861
ReflectionResolution: 2.3→20 Å / Num. all: 10405 / Num. obs: 9635 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17 % / Rsym value: 0.052
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 14 / Num. unique all: 840 / Rsym value: 0.085 / % possible all: 80.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 488 -random
Rwork0.187 ---
all-10405 --
obs-9165 88.1 %-
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1471 0 14 131 1616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.29
LS refinement shellResolution: 2.3→2.39 Å /
RfactorNum. reflection
Rfree0.278 45
Rwork0.202 -
obs-871

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