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- PDB-3p3d: Crystal structure of the Nup53 RRM domain from Pichia guilliermondii -

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Basic information

Entry
Database: PDB / ID: 3p3d
TitleCrystal structure of the Nup53 RRM domain from Pichia guilliermondii
ComponentsNucleoporin 53
KeywordsNUCLEAR PROTEIN / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / Protein Transport / component of Nuclear Pore Complex / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


structural constituent of nuclear pore / mRNA transport / nuclear pore / protein transport / nuclear membrane / nucleic acid binding
Similarity search - Function
RNA-recognition motif (RRM) Nup35-type domain / Nucleoporin, NUP53 / Nup53/35/40-type RNA recognition motif / RNA-recognition motif (RRM) Nup35-type domain profile. / RRM (RNA recognition motif) domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RRM Nup35-type domain-containing protein
Similarity search - Component
Biological speciesPichia guilliermondii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSampathkumar, P. / Shawn, C. / Bain, K. / Gilmore, J. / Gheyi, T. / Atwell, S. / Thompson, D.A. / Emtage, J.S. / Wasserman, S. / Sauder, J.M. ...Sampathkumar, P. / Shawn, C. / Bain, K. / Gilmore, J. / Gheyi, T. / Atwell, S. / Thompson, D.A. / Emtage, J.S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of the Nup53 RRM domain from Pichia guilliermondii
Authors: Sampathkumar, P.
History
DepositionOct 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 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

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Assembly

Deposited unit
A: Nucleoporin 53


Theoretical massNumber of molelcules
Total (without water)14,5171
Polymers14,5171
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nucleoporin 53

A: Nucleoporin 53


Theoretical massNumber of molelcules
Total (without water)29,0352
Polymers29,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area1240 Å2
ΔGint-14 kcal/mol
Surface area8950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.507, 62.507, 55.117
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Nucleoporin 53 /


Mass: 14517.317 Da / Num. of mol.: 1 / Fragment: RRM Domain residues 261-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichia guilliermondii (fungus) / Gene: NUP53 (gi146415668), PGUG_04532 / Plasmid: BC-pSGX3(BC); modified pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: A5DMN1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 100mM sodium acetate, 20% PEG 1500, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 24, 2010
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.35→38.62 Å / Num. obs: 5437 / % possible obs: 99.8 % / Redundancy: 21 % / Biso Wilson estimate: 59 Å2 / Rsym value: 0.085 / Net I/σ(I): 21.1
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 21.9 % / Mean I/σ(I) obs: 6.5 / Num. unique all: 782 / Rsym value: 0.406 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Poly-Ala of 1WWH

1wwh


Resolution: 2.35→20.46 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.577 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.353 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2876 742 13.7 %RANDOM
Rwork0.2379 ---
obs0.2447 5403 99.76 %-
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 max: 75.06 Å2 / Biso mean: 45.3917 Å2 / Biso min: 29.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms668 0 0 20 688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022684
X-RAY DIFFRACTIONr_bond_other_d0.0010.02434
X-RAY DIFFRACTIONr_angle_refined_deg1.421.958935
X-RAY DIFFRACTIONr_angle_other_deg0.87431061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.111585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90924.48329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8461597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.663152
X-RAY DIFFRACTIONr_chiral_restr0.0740.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02144
X-RAY DIFFRACTIONr_mcbond_it0.7111.5432
X-RAY DIFFRACTIONr_mcbond_other0.1261.5174
X-RAY DIFFRACTIONr_mcangle_it1.3822695
X-RAY DIFFRACTIONr_scbond_it1.8493252
X-RAY DIFFRACTIONr_scangle_it3.1414.5240
LS refinement shellResolution: 2.353→2.413 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 45 -
Rwork0.367 339 -
all-384 -
obs--100 %

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