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- PDB-6rpq: Crystal structure of PhoCDC21-1 intein -

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Basic information

Entry
Database: PDB / ID: 6rpq
TitleCrystal structure of PhoCDC21-1 intein
ComponentsUbiquitin-like protein SMT3,1108aa long hypothetical cell division control protein
KeywordsHYDROLASE / intein / protein-splicing / HINT
Function / homology
Function and homology information


SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / intein-mediated protein splicing / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / DNA replication initiation / DNA helicase activity / condensed nuclear chromosome / PML body / protein tag activity / DNA helicase / cell division / DNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
Intein splicing domain / Intein / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / MCM N-terminal domain / MCM N-terminal domain ...Intein splicing domain / Intein / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / MCM N-terminal domain / MCM N-terminal domain / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA helicase / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Pyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.654 Å
AuthorsBeyer, H.M. / Mikula, K.M. / Iwai, H.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland137995, 277335 Finland
Novo Nordisk FoundationNNF17OC0025402 Finland
Sigrid Juselius Foundation Finland
Citation
Journal: Extremophiles / Year: 2019
Title: Crystal structures of CDC21-1 inteins from hyperthermophilic archaea reveal the selection mechanism for the highly conserved homing endonuclease insertion site.
Authors: Beyer, H.M. / Mikula, K.M. / Kudling, T.V. / Iwai, H.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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: Ubiquitin-like protein SMT3,1108aa long hypothetical cell division control protein


Theoretical massNumber of molelcules
Total (without water)32,2631
Polymers32,2631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.920, 100.920, 91.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Ubiquitin-like protein SMT3,1108aa long hypothetical cell division control protein


Mass: 32263.498 Da / Num. of mol.: 1 / Mutation: A101T, C112A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 204508 / S288c, ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: SMT3, YDR510W, D9719.15, PH0606 / Plasmid: pCARSF52 / Production host: Escherichia coli (E. coli) / Variant (production host): T7 Express / References: UniProt: Q12306, UniProt: O58310

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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: 3.62 Å3/Da / Density % sol: 66.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: tri-ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 14, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.65→50.46 Å / Num. obs: 13373 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rrim(I) all: 0.094 / Net I/σ(I): 18.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.8114.21.2421540.7131.67999.9
2.81-3.0113.72.6220110.9230.86100

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXmodel building
PHENIX(1.15.1_3469: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUV, 6RPP

1euv

6rpp


Resolution: 2.654→50.46 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 33.12
RfactorNum. reflection% reflection
Rfree0.2352 669 5.01 %
Rwork0.2023 --
obs0.204 13363 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.654→50.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 0 0 2037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042075
X-RAY DIFFRACTIONf_angle_d0.8872791
X-RAY DIFFRACTIONf_dihedral_angle_d4.0061278
X-RAY DIFFRACTIONf_chiral_restr0.059301
X-RAY DIFFRACTIONf_plane_restr0.006364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6536-2.85840.40791330.34622524X-RAY DIFFRACTION100
2.8584-3.14610.36711330.28382525X-RAY DIFFRACTION100
3.1461-3.60120.29181330.24192526X-RAY DIFFRACTION100
3.6012-4.53670.23451340.18312535X-RAY DIFFRACTION100
4.5367-50.46910.18811360.17812584X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.99560.78460.95875.84131.20634.7163-0.74180.9996-0.3165-1.09910.9637-1.6214-0.95520.99-0.11551.1263-0.32230.26971.3144-0.30611.29818.529336.1659-21.8686
23.42821.44911.1337.06452.17433.5084-0.0815-0.00570.3087-0.2723-0.03040.2265-0.44010.02830.07020.803-0.0160.07810.7459-0.03910.7532-12.243219.7106-29.4462
32.7519-0.75360.82356.68341.12742.48620.0412-0.52790.03890.1481-0.00360.4784-0.0389-0.2203-0.07020.68760.00990.04490.8210.0170.6721-15.031910.0015-22.3985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 103 )
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 142 )
3X-RAY DIFFRACTION3chain 'A' and (resid 143 through 279 )

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