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- PDB-6mx6: The Prp8 intein of Cryptococcus neoformans -

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Basic information

Entry
Database: PDB / ID: 6mx6
TitleThe Prp8 intein of Cryptococcus neoformans
ComponentsPre-mRNA-processing-splicing factor 8
KeywordsHYDROLASE / Prp8 / intein / cryptococcus neoformans
Function / homology
Function and homology information


U5 snRNA binding / U6 snRNA binding / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity
Similarity search - Function
Hint domain superfamily / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 ...Hint domain superfamily / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Pre-mRNA-processing-splicing factor 8
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.749 Å
AuthorsLi, Z. / Li, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM39422 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM44844 United States
CitationJournal: Plos Biol. / Year: 2019
Title: Spliceosomal Prp8 intein at the crossroads of protein and RNA splicing.
Authors: Green, C.M. / Li, Z. / Smith, A.D. / Novikova, O. / Bacot-Davis, V.R. / Gao, F. / Hu, S. / Banavali, N.K. / Thiele, D.J. / Li, H. / Belfort, M.
History
DepositionOct 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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: Pre-mRNA-processing-splicing factor 8
B: Pre-mRNA-processing-splicing factor 8
C: Pre-mRNA-processing-splicing factor 8
D: Pre-mRNA-processing-splicing factor 8
E: Pre-mRNA-processing-splicing factor 8
F: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)120,5556
Polymers120,5556
Non-polymers00
Water9,908550
1
A: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)20,0921
Polymers20,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)20,0921
Polymers20,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)20,0921
Polymers20,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)20,0921
Polymers20,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)20,0921
Polymers20,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)20,0921
Polymers20,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.153, 63.226, 80.204
Angle α, β, γ (deg.)103.320, 95.530, 117.340
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Pre-mRNA-processing-splicing factor 8


Mass: 20092.473 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_00147 / Production host: Escherichia coli (E. coli) / References: UniProt: J9VI50
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 28% PEG4,000, 0.1 M sodium acetate, pH 4.2, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.75→100 Å / Num. obs: 90650 / % possible obs: 86.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.055 / Rrim(I) all: 0.089 / Χ2: 1.416 / Net I/σ(I): 10.6 / Num. measured all: 212046
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.782.30.97544030.4670.7751.2510.52884
1.78-1.812.30.87540270.5610.6831.1140.54576.5
1.81-1.852.40.74745160.6290.5810.950.59286.4
1.85-1.892.40.55346740.7080.4230.6980.60989.2
1.89-1.932.40.46747480.7530.3580.5910.789.7
1.93-1.972.40.35546410.8360.2730.450.80388.3
1.97-2.022.40.2945800.8810.2220.3660.90987.4
2.02-2.072.40.22744880.9130.1740.2871.01985.8
2.07-2.142.40.19344130.9410.1480.2441.21783.9
2.14-2.22.40.15841150.9570.1220.21.40977.6
2.2-2.282.40.13747200.9640.1050.1731.4290.3
2.28-2.382.40.10947130.9790.0840.1381.46189.9
2.38-2.482.40.10246640.980.0790.131.71189
2.48-2.612.40.08546600.9860.0660.1091.95388
2.61-2.782.30.07343190.9880.0590.0942.22982.2
2.78-2.992.30.05445680.9920.0450.0712.29786.7
2.99-3.292.30.04147180.9960.0340.0542.43490.1
3.29-3.772.20.03746210.9950.030.0482.50788
3.77-4.752.20.03144030.9960.0250.042.31883.9
4.75-1002.20.0346590.9970.0250.042.12788.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.1 Å32.27 Å
Translation2.1 Å32.27 Å

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.7.16phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MWY

6mwy


Resolution: 1.749→32.692 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 1982 2.19 %
Rwork0.1974 --
obs0.1982 90489 85.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.27 Å2 / Biso mean: 30.387 Å2 / Biso min: 11.24 Å2
Refinement stepCycle: final / Resolution: 1.749→32.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7020 0 0 550 7570
Biso mean---37.8 -
Num. residues----858

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