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- PDB-2hhl: Crystal structure of the human small CTD phosphatase 3 isoform 1 -

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Basic information

Entry
Database: PDB / ID: 2hhl
TitleCrystal structure of the human small CTD phosphatase 3 isoform 1
ComponentsCTD small phosphatase-like protein
KeywordsHYDROLASE / CTD phosphatase / Keggins anion / Structural Genomics / PSI / 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 / negative regulation of G1/S transition of mitotic cell cycle / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / negative regulation of protein phosphorylation / extracellular exosome / 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
12-TUNGSTOPHOSPHATE / CTD small phosphatase-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMalashkevich, V.N. / Toro, R. / Ramagopal, U. / Sauder, J.M. / Schwinn, K.D. / Thompson, D.A. / Rutter, M.E. / Dickey, M. / Groshong, C. / Bain, K.T. ...Malashkevich, V.N. / Toro, R. / Ramagopal, U. / Sauder, J.M. / Schwinn, K.D. / Thompson, D.A. / Rutter, M.E. / Dickey, M. / Groshong, C. / Bain, K.T. / Adams, J.M. / Reyes, C. / Rooney, I. / Powell, A. / Boice, A. / Gheyi, T. / Ozyurt, S. / Atwell, S. / Wasserman, S.R. / Emtage, S. / 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
DepositionJun 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: CTD small phosphatase-like protein
B: CTD small phosphatase-like protein
C: CTD small phosphatase-like protein
D: CTD small phosphatase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3307
Polymers89,6984
Non-polymers8,6313
Water9,728540
1
A: CTD small phosphatase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3022
Polymers22,4251
Non-polymers2,8771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CTD small phosphatase-like protein


Theoretical massNumber of molelcules
Total (without water)22,4251
Polymers22,4251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CTD small phosphatase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3022
Polymers22,4251
Non-polymers2,8771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CTD small phosphatase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3022
Polymers22,4251
Non-polymers2,8771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.419, 49.857, 179.747
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CTD small phosphatase-like protein / CTDSP-like / Small C-terminal domain phosphatase 3 / Small CTD phosphatase 3 / SCP3 / Nuclear LIM ...CTDSP-like / Small C-terminal domain phosphatase 3 / Small CTD phosphatase 3 / SCP3 / Nuclear LIM interactor-interacting factor 1 / NLI-interacting factor 1 / NIF-like protein / RBSP3 / YA22 protein / HYA22


Mass: 22424.609 Da / Num. of mol.: 4 / Fragment: residues 82-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTDSPL, C3orf8, NIF1, NIFL, YA22 / Production host: Escherichia coli (E. coli) / References: UniProt: O15194
#2: Chemical ChemComp-KEG / 12-TUNGSTOPHOSPHATE


Mass: 2877.030 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O40PW12
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M lithium sulfate monohydrate, 0.1M bis-tris, 25% w/v PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.74 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2006
RadiationMonochromator: X6A / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionRedundancy: 1.7 % / Av σ(I) over netI: 8.5 / Number: 139989 / Rmerge(I) obs: 0.056 / Χ2: 1.05 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 84087 / % possible obs: 87.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.525094.910.0431.1491.7
3.594.529510.0381.1291.7
3.143.599210.0420.9661.7
2.853.148910.0530.951.7
2.652.858810.0740.9451.7
2.492.6586.710.0971.0421.7
2.372.4986.110.1291.0541.7
2.262.3785.810.1641.1141.7
2.182.2685.410.2061.1131.7
2.12.187410.2650.9741.4
ReflectionResolution: 2.1→20 Å / Num. obs: 47666 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Χ2: 1.048 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.265 / Num. unique all: 7128 / Χ2: 0.974 / % possible all: 74

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Phasing

Phasing MRRfactor: 0.499 / Cor.coef. Fo:Fc: 0.509
Highest resolutionLowest resolution
Rotation3 Å33.09 Å
Translation3 Å33.09 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TA0

1ta0


Resolution: 2.1→19.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.986 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.237 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2386 5 %RANDOM
Rwork0.188 ---
all0.191 49147 --
obs0.191 47398 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.238 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5774 0 158 540 6472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0226142
X-RAY DIFFRACTIONr_angle_refined_deg3.1992.0448701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6365711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66823.453278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44115980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8781541
X-RAY DIFFRACTIONr_chiral_restr0.1840.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024517
X-RAY DIFFRACTIONr_nbd_refined0.2240.22501
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23942
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2516
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.2148
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.224
X-RAY DIFFRACTIONr_mcbond_it1.1131.53707
X-RAY DIFFRACTIONr_mcangle_it1.77425877
X-RAY DIFFRACTIONr_scbond_it2.75432872
X-RAY DIFFRACTIONr_scangle_it3.7864.52626
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 169 -
Rwork0.228 3014 -
obs-3183 87.81 %

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