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- PDB-3pgg: Crystal structure of cryptosporidium parvum u6 snrna-associated s... -

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Basic information

Entry
Database: PDB / ID: 3pgg
TitleCrystal structure of cryptosporidium parvum u6 snrna-associated sm-like protein lsm5
ComponentsU6 snRNA-associated Sm-like protein LSm5. SM domain
KeywordsDNA BINDING PROTEIN / U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN / LSM5 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Lsm1-7-Pat1 complex / U6 snRNP / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / mRNA splicing, via spliceosome / RNA binding
Similarity search - Function
Sm-like protein LSm5 / SH3 type barrels. - #100 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
U6 snRNA-associated Sm-like protein LSm5
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsDong, A. / Gao, M. / Zhao, Y. / Lew, J. / Wasney, G.A. / Kozieradzki, I. / Vedadi, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. ...Dong, A. / Gao, M. / Zhao, Y. / Lew, J. / Wasney, G.A. / Kozieradzki, I. / Vedadi, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Artz, J. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-Scale Protein Expression and Structural Biology of Plasmodium Falciparum and Related Apicomplexan Organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionNov 1, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 2, 2011ID: 2FWK
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 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: U6 snRNA-associated Sm-like protein LSm5. SM domain
B: U6 snRNA-associated Sm-like protein LSm5. SM domain


Theoretical massNumber of molelcules
Total (without water)26,6002
Polymers26,6002
Non-polymers00
Water48627
1
A: U6 snRNA-associated Sm-like protein LSm5. SM domain
B: U6 snRNA-associated Sm-like protein LSm5. SM domain

A: U6 snRNA-associated Sm-like protein LSm5. SM domain
B: U6 snRNA-associated Sm-like protein LSm5. SM domain

A: U6 snRNA-associated Sm-like protein LSm5. SM domain
B: U6 snRNA-associated Sm-like protein LSm5. SM domain


Theoretical massNumber of molelcules
Total (without water)79,8006
Polymers79,8006
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9110 Å2
ΔGint-61 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.163, 101.163, 49.092
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsHEXAMERIC

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Components

#1: Protein U6 snRNA-associated Sm-like protein LSm5. SM domain


Mass: 13300.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: cgd7_4580 / Plasmid: P28-LIC-THROMBIN DERIVED FROM PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON PLUS RIL / References: UniProt: Q5CXX3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 1.05 M NA CITRATE, 100 MM BISTRIS PH6.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 25, 2005 / Details: VERIMAX HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.601
11h+k,-k,-l20.399
ReflectionResolution: 2.14→50 Å / Num. all: 16363 / Num. obs: 16363 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 54.88
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.87 / Num. unique all: 866 / Rsym value: 0.795 / % possible all: 84.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASERV. 1.3.1phasing
REFMAC5.5.0109refinement
Coot0.6model building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.261 / SU ML: 0.207 / Isotropic thermal model: 1M8V / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25783 809 5 %RANDOM
Rwork0.21398 ---
obs0.216 15457 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.076 Å2
Baniso -1Baniso -2Baniso -3
1--5.84 Å20 Å20 Å2
2---5.84 Å20 Å2
3---11.68 Å2
Refinement stepCycle: LAST / Resolution: 2.14→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1154 0 0 27 1181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221166
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9871578
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3735154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88925.65246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03115186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.45154
X-RAY DIFFRACTIONr_chiral_restr0.1170.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021862
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_it2.011.5772
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.18621221
X-RAY DIFFRACTIONr_scbond_it4.6063394
X-RAY DIFFRACTIONr_scangle_it6.7734.5357
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.192 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 64 -
Rwork0.215 1083 -
obs--96.14 %

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