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- PDB-2q5e: Crystal structure of human carboxy-terminal domain RNA polymerase... -

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Basic information

Entry
Database: PDB / ID: 2q5e
TitleCrystal structure of human carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
ComponentsCarboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat phosphatase activity / XBP1(S) activates chaperone genes / negative regulation of G1/S transition of mitotic cell cycle / myosin phosphatase activity / protein-serine/threonine phosphatase / protein dephosphorylation / negative regulation of protein phosphorylation / nucleoplasm / 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 ...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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Lau, C. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Struct.Funct.Genom. / Year: 2007
Title: Structural genomics of protein phosphatases.
Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 2
B: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
C: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
D: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
E: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
F: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
G: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
H: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,11616
Polymers169,9228
Non-polymers1948
Water1,63991
1
A: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2652
Polymers21,2401
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2652
Polymers21,2401
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2652
Polymers21,2401
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2652
Polymers21,2401
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2652
Polymers21,2401
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2652
Polymers21,2401
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2652
Polymers21,2401
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2652
Polymers21,2401
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.643, 117.637, 170.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2 / Small CTD phosphatase 2 / SCP2 / Nuclear LIM interactor-interacting factor 2 / NLI-interacting ...Small CTD phosphatase 2 / SCP2 / Nuclear LIM interactor-interacting factor 2 / NLI-interacting factor 2 / Protein OS-4


Mass: 21240.197 Da / Num. of mol.: 8 / Fragment: Residues 87-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTDSP2, NIF2, OS4 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O14595, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 2.8 M Sodium acetate, pH 7.0, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2007
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.51→96.76 Å / Num. all: 72419 / Num. obs: 72419 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 56.1 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 18.6
Reflection shellResolution: 2.51→2.65 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.6 / Num. unique all: 8821 / Rsym value: 0.447 / % possible all: 81.7

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
DENZOdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.51→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.891 / SU B: 10.246 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.402 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 3629 5 %RANDOM
Rwork0.216 ---
obs0.219 72246 96.38 %-
all-72246 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.075 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11467 0 8 91 11566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02211709
X-RAY DIFFRACTIONr_angle_refined_deg2.0841.97715901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2851413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30923.715576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.709151977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6851593
X-RAY DIFFRACTIONr_chiral_restr0.1410.21825
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028905
X-RAY DIFFRACTIONr_nbd_refined0.2430.25052
X-RAY DIFFRACTIONr_nbtor_refined0.330.27926
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2515
X-RAY DIFFRACTIONr_metal_ion_refined0.0220.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3820.27
X-RAY DIFFRACTIONr_mcbond_it1.2251.57294
X-RAY DIFFRACTIONr_mcangle_it2.059211605
X-RAY DIFFRACTIONr_scbond_it3.06734891
X-RAY DIFFRACTIONr_scangle_it4.7164.54296
LS refinement shellResolution: 2.51→2.574 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 227 -
Rwork0.323 3860 -
obs-4087 75.8 %

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