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- PDB-6owu: THE PRP8 INTEIN OF CRYPTOCOCCUS NEOFORMANS in complex with Zn2+ -

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Basic information

Entry
Database: PDB / ID: 6owu
TitleTHE PRP8 INTEIN OF CRYPTOCOCCUS NEOFORMANS in complex with Zn2+
ComponentsPRP8 protein
KeywordsHYDROLASE / Prp8 Intein
Function / homologyprotein splicing / Hom-end-associated Hint / Hom_end-associated Hint / Hint domain superfamily / Pre-mRNA-processing-splicing factor 8 / spliceosomal complex / mRNA splicing, via spliceosome / PRP8 protein
Function and homology information
Biological speciesCryptococcus neoformans var. grubii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsLi, Z. / Li, H.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI140726 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI141178 United States
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
DepositionMay 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRP8 protein
B: PRP8 protein
C: PRP8 protein
D: PRP8 protein
E: PRP8 protein
F: PRP8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,57015
Polymers126,9826
Non-polymers5899
Water10,124562
1
A: PRP8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2292
Polymers21,1641
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PRP8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2943
Polymers21,1641
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PRP8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2292
Polymers21,1641
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PRP8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2943
Polymers21,1641
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: PRP8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2292
Polymers21,1641
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: PRP8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2943
Polymers21,1641
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.093, 63.039, 78.636
Angle α, β, γ (deg.)94.86, 103.13, 117.44
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PRP8 protein /


Mass: 21163.627 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii (fungus)
Gene: PRP8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6TER0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.08 Å3/Da / Density % sol: 40.78 %
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: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC HF-4M / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.84→40.09 Å / Num. obs: 71327 / % possible obs: 80.43 % / Redundancy: 2.4 % / Biso Wilson estimate: 20.6 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.0844 / Rpim(I) all: 0.0639 / Rrim(I) all: 0.1065 / Rsym value: 0.0844 / Net I/σ(I): 9.38
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6013 / CC1/2: 0.654 / Rpim(I) all: 0.374 / Rrim(I) all: 0.606 / Rsym value: 0.473 / % possible all: 67.6

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→40.089 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.38
RfactorNum. reflection% reflection
Rfree0.2427 2011 2.82 %
Rwork0.1988 --
obs0.2 71311 80.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.84→40.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7020 0 9 562 7591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067177
X-RAY DIFFRACTIONf_angle_d0.8939677
X-RAY DIFFRACTIONf_dihedral_angle_d4.3856112
X-RAY DIFFRACTIONf_chiral_restr0.051087
X-RAY DIFFRACTIONf_plane_restr0.0051262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8396-1.88560.2938980.2763755X-RAY DIFFRACTION61
1.8856-1.93660.3061480.26195170X-RAY DIFFRACTION84
1.9366-1.99360.26841630.23715285X-RAY DIFFRACTION86
1.9936-2.0580.31021410.2265216X-RAY DIFFRACTION85
2.058-2.13150.26281520.20874965X-RAY DIFFRACTION81
2.1315-2.21680.25741440.19875167X-RAY DIFFRACTION84
2.2168-2.31770.24541560.19575054X-RAY DIFFRACTION82
2.3177-2.43990.24581320.19384599X-RAY DIFFRACTION75
2.4399-2.59280.24611410.18614705X-RAY DIFFRACTION77
2.5928-2.79290.27061420.19555411X-RAY DIFFRACTION88
2.7929-3.07390.23791560.19514989X-RAY DIFFRACTION81
3.0739-3.51840.2011500.18255251X-RAY DIFFRACTION85
3.5184-4.43190.19661330.16924606X-RAY DIFFRACTION75
4.4319-40.09820.25681550.21065127X-RAY DIFFRACTION83

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