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- PDB-3odr: Crystal Structure of the N-terminal Domain of Human Symplekin -

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Basic information

Entry
Database: PDB / ID: 3odr
TitleCrystal Structure of the N-terminal Domain of Human Symplekin
ComponentsSymplekin
KeywordsPROTEIN BINDING / Heat Domain / Scaffold
Function / homology
Function and homology information


nuclear stress granule / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / RNA Polymerase II Transcription Termination / : / Processing of Capped Intron-Containing Pre-mRNA / bicellular tight junction / negative regulation of protein binding ...nuclear stress granule / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / RNA Polymerase II Transcription Termination / : / Processing of Capped Intron-Containing Pre-mRNA / bicellular tight junction / negative regulation of protein binding / nuclear body / cytoskeleton / cell adhesion / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Symplekin/Pta1 / Symplekin C-terminal / Symplekin/Pta1, N-terminal / Symplekin/PTA1 N-terminal / Symplekin tight junction protein C terminal / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTong, L. / Xiang, K.
CitationJournal: Nature / Year: 2010
Title: Crystal structure of the human symplekin-Ssu72-CTD phosphopeptide complex.
Authors: Xiang, K. / Nagaike, T. / Xiang, S. / Kilic, T. / Beh, M.M. / Manley, J.L. / Tong, L.
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: Symplekin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2692
Polymers46,2071
Non-polymers621
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.768, 43.910, 64.284
Angle α, β, γ (deg.)78.67, 78.60, 73.26
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Symplekin


Mass: 46206.789 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYMPK, SPK / Production host: Escherichia coli (E. coli) / References: UniProt: Q92797
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.91 Å3/Da / Density % sol: 35.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50MM BIS-TRIS, 40MM AMMONIUM SULFATE, 40% (V/V) PENTAERYTHRITOL ETHOXYLATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 17076 / % possible obs: 96.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.2409
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 3.311 / % possible all: 96.9

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Processing

Software
NameVersionClassification
CBASSdata collection
COMOphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 12.23 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 864 5.1 %RANDOM
Rwork0.18639 ---
obs0.18857 15934 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.446 Å2
Baniso -1Baniso -2Baniso -3
1-3.97 Å21.48 Å22.1 Å2
2---2.66 Å20.32 Å2
3----3.12 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 4 73 2585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222547
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9813449
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0165316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08725108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95515491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8381516
X-RAY DIFFRACTIONr_chiral_restr0.0960.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211832
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.881.51589
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78322589
X-RAY DIFFRACTIONr_scbond_it3.2423958
X-RAY DIFFRACTIONr_scangle_it5.5894.5860
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.318 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.289 140 -
Rwork0.206 2315 -
obs--96.65 %
Refinement TLS params.Method: refined / Origin x: -0.1054 Å / Origin y: -0.5346 Å / Origin z: 0.7763 Å
111213212223313233
T0.0294 Å2-0.0288 Å20.002 Å2-0.0756 Å2-0.005 Å2--0.1068 Å2
L0.3163 °2-0.0902 °20.0513 °2-0.7412 °2-0.3549 °2--2.0417 °2
S-0.003 Å °-0.0673 Å °-0.0145 Å °0.0715 Å °-0.0232 Å °0.0287 Å °0.1043 Å °0.0238 Å °0.0262 Å °

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