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- PDB-6rpp: Crystal structure of PabCDC21-1 intein -

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Basic information

Entry
Database: PDB / ID: 6rpp
TitleCrystal structure of PabCDC21-1 intein
ComponentsCell division control protein
KeywordsHYDROLASE / intein / protein-splicing / HINT
Function / homology
Function and homology information


intein-mediated protein splicing / DNA replication initiation / DNA helicase activity / DNA helicase / cell division / DNA binding / ATP binding
Similarity search - Function
Intein splicing domain / Intein / 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 / MCM OB domain / MCM OB domain ...Intein splicing domain / Intein / 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 / MCM OB domain / MCM OB domain / Intein N-terminal splicing region / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / Intein N-terminal splicing motif profile. / minichromosome maintenance proteins / MCM domain / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / DNA helicase
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMikula, K.M. / Beyer, H.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

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1663
Polymers19,0011
Non-polymers1652
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint2 kcal/mol
Surface area8970 Å2
Unit cell
Length a, b, c (Å)75.481, 93.588, 49.746
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-201-

ACT

21A-201-

ACT

31A-411-

HOH

41A-429-

HOH

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Components

#1: Protein Cell division control protein / MCM inteins containing helicase / minichromosome maintenance protein


Mass: 19000.789 Da / Num. of mol.: 1 / Mutation: C1A, N164A
Source method: isolated from a genetically manipulated source
Details: Including three residues of N-terminal "Ser-Ala-Lys", and one residue C-terminal "Ala" extein sequences.
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Gene: cdc21, PAB2373 / Plasmid: pBHRSF399 / Production host: Escherichia coli (E. coli) / Variant (production host): T7 Express / References: UniProt: Q9UYR7
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: sodium acetate, polyethylene glycol 4000, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 11, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→29.38 Å / Num. obs: 23504 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 22.45 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.059 / Net I/σ(I): 24.37
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 3.58 / Num. unique obs: 3723 / CC1/2: 0.929 / Rrim(I) all: 0.595 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
ARP/wARPmodel building
Cootmodel building
PHENIX1.15.1_3469refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O1S

4o1s


Resolution: 1.6→29.38 Å / SU ML: 0.1864 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.2505
RfactorNum. reflection% reflection
Rfree0.2178 1178 5.01 %
Rwork0.1782 --
obs0.1802 23498 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.9 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1339 0 11 132 1482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01391397
X-RAY DIFFRACTIONf_angle_d1.3841885
X-RAY DIFFRACTIONf_chiral_restr0.0848204
X-RAY DIFFRACTIONf_plane_restr0.0094245
X-RAY DIFFRACTIONf_dihedral_angle_d6.33051181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.680.24551600.22192735X-RAY DIFFRACTION99.45
1.68-1.760.25731210.2052770X-RAY DIFFRACTION99.93
1.76-1.880.23231540.19832740X-RAY DIFFRACTION100
1.88-2.020.23011350.18542770X-RAY DIFFRACTION100
2.02-2.220.2331360.18142793X-RAY DIFFRACTION100
2.22-2.540.22581450.18242782X-RAY DIFFRACTION100
2.54-3.210.19491600.18722807X-RAY DIFFRACTION99.97
3.21-29.380.21471670.16112923X-RAY DIFFRACTION99.97
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)
13.26365502092-0.829336452975-0.7181301453072.76443631025-0.5545044551184.5072115125-0.09336914930480.02596974203150.101431640483-0.02104672034260.094633929088-0.20603131621-0.2106822823810.242067880756-0.05232000661580.1748605170460.001487180891610.004938907390880.1380462479060.007625484206860.1890224850423.201063139918.863588538918.8748596234
24.04717899937-0.985283350621-1.868011303133.73540991538-0.07950334279044.333523978270.03217260757490.417753327709-0.160637284003-0.420931200602-0.283785978078-0.1720105320650.1961746420460.1066026426640.07304352338970.2212087321850.03623174596590.02056445378120.2346454430580.01109574797470.22276289529329.160733213412.20036987646.96367898641
35.172191396911.92379020295-3.128560990163.24898034323-1.774028077664.29529199753-0.0878563669029-0.399720059957-0.3541567867880.479914538926-0.135768187289-0.31640864980.1828731220380.4210469276890.2313819878160.2834659561810.0241300788594-0.03852136652530.1908906171960.03739028252730.22261223545920.62170540026.8106621351129.5733237482
42.884420059-1.516938624240.211135355123.75969721518-1.330666027376.3905170871-0.05581007262160.0535448125006-0.0693104669565-0.0846075129498-0.278451567249-0.2868432459280.5857271525860.6213720817340.07050255480210.138566562412-0.037891590374-0.00215042101220.1291134068140.006051359489160.22314023665724.10071560468.9005976731617.1251047921
52.36660271499-0.0140890213948-0.3884702528832.037533668910.5168702619717.575006357030.0625637885402-0.06824879719210.141738382133-0.03333174743850.00354088548040.208551023024-0.392574170924-0.3542434598570.06462843365120.1411493382040.0170258995862-0.03042729619820.1497681934120.01003508688270.1730309874359.535747809620.874012020817.2585739821
63.885370947250.392050930456-1.227088075125.77815036784-2.551479021164.874937880760.0976862232614-0.398205120781-0.364794284690.177629564407-0.1877885331330.7402807122830.766735042736-0.7128217403990.02747984177550.270003806681-0.09215148335880.03613033218380.3174057703910.03673817332620.336462561154.660602857979.1463992562223.2009298371
71.44956875142-0.0939491715589-0.4366974144541.35616007995-0.7083929864722.48370575546-0.0275936307661-0.0466036011208-0.1093717126460.04928399490530.006993204305510.1603421093650.0167759883406-0.2166509459420.0153687732570.15833789379-0.0215341405739-0.01319841883330.148437305591-0.007846548882980.18158778907412.910352659316.070372279521.8678800704
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 72 )
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 94 )
6X-RAY DIFFRACTION6chain 'A' and (resid 95 through 111 )
7X-RAY DIFFRACTION7chain 'A' and (resid 112 through 165 )

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