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- PDB-6riz: Crystal structure of gp41-1 intein (C1A, F65W, D107C) -

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Basic information

Entry
Database: PDB / ID: 6riz
TitleCrystal structure of gp41-1 intein (C1A, F65W, D107C)
Componentsgp41-1 intein
KeywordsHYDROLASE / intein / protein-splicing / SPLICING
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBeyer, H.M. / Lountos, G.T. / Mikula, M.K. / Wlodawer, A. / Iwai, H.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland137995, 277335 Finland
Novo Nordisk FoundationNNF17OC0025402 Finland
Sigrid Juselius Foundation Finland
CitationJournal: Int J Mol Sci / Year: 2020
Title: The Convergence of the Hedgehog/Intein Fold in Different Protein Splicing Mechanisms.
Authors: Beyer, H.M. / Virtanen, S.I. / Aranko, A.S. / Mikula, K.M. / Lountos, G.T. / Wlodawer, A. / Ollila, O.H.S. / Iwai, H.
History
DepositionApr 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: gp41-1 intein


Theoretical massNumber of molelcules
Total (without water)14,4381
Polymers14,4381
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.220, 90.220, 71.734
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-246-

HOH

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Components

#1: Protein gp41-1 intein


Mass: 14437.579 Da / Num. of mol.: 1 / Mutation: C1A, F65W, D107C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Plasmid: pHBRSF044 / Production host: Escherichia coli (E. coli) / Variant (production host): T7 Express
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: bis-tris pH 5.5, ammonium sulfate, polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 22, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 15226 / % possible obs: 100 % / Redundancy: 33.5 % / CC1/2: 1 / Rmerge(I) obs: 0.117 / Net I/σ(I): 33
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 741 / CC1/2: 0.554 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIX1.16_3549model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QAZ

6qaz


Resolution: 1.85→45.11 Å / SU ML: 0.2118 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 18.1182
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2023 717 4.73 %
Rwork0.1699 14430 -
obs0.1714 15147 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.89 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 157 1158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661045
X-RAY DIFFRACTIONf_angle_d0.91411412
X-RAY DIFFRACTIONf_chiral_restr0.0558162
X-RAY DIFFRACTIONf_plane_restr0.0037181
X-RAY DIFFRACTIONf_dihedral_angle_d3.2395897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.990.25531300.21612829X-RAY DIFFRACTION99.76
1.99-2.190.23421280.17842841X-RAY DIFFRACTION100
2.19-2.510.2081610.1762845X-RAY DIFFRACTION100
2.51-3.160.23361450.18332889X-RAY DIFFRACTION99.97
3.16-45.10.1681530.14943026X-RAY DIFFRACTION98.54
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)
11.906376530311.999840688980.5717239952883.71011790408-2.639323343158.12573972216-0.110373567272-0.0108391290909-0.158518335184-0.1378313033620.0188603172382-0.05507009391030.2293925884210.084675553290.03205872229640.1247871233640.02567809481780.02036978371370.124343188586-0.02004364824750.1850317942876.6173674247118.53854410414.56117554421
22.960246718941.100257650971.594698617362.758375133851.103305443586.261521543930.0178512613807-0.110385937524-0.1606643550830.140704056288-0.08622701922590.1018273281580.0535135328632-0.4086785073790.04699244619590.123313146622-0.005699625943770.02349580076630.1195735026790.01927677435830.165702153259-1.2379869061221.30754437778.50181639607
32.769931392842.851426701493.983908716384.894869775452.982928823527.21569997633-0.2060884816030.007930104300690.100898988481-0.3728581893380.169387594221-0.216920716773-0.4553279328650.362699030114-0.04196736927640.206172975304-0.06248757257880.03207753862450.215488475075-0.03787258575520.17115065395611.524841643328.0699022196-4.70450293331
44.47024835925-1.64786256501-3.86207789142.137932496651.788895919133.440814721850.1369516156250.169494133160.38852587704-0.427441464217-0.222194914071-0.00719708374514-0.712302420643-0.006881337248350.1401834248160.370620931566-0.00996239669956-0.03223303769430.1467409557740.05089599943620.2179703585284.5775274514537.09735140230.262521721381
53.53449166591.03385540812-0.9729257606562.11518765664-0.1025921486221.332295549690.133835908201-0.1214343090520.153839252152-0.1246979413650.0452670745721-0.11154491723-0.7250334420480.528450353251-0.1326984666910.429125203847-0.138035670898-0.002190670372170.1756078749170.00259192915330.22036337973712.490797254737.16836652872.71085456121
63.10788203872-0.171620810541-2.725376697465.32929319001-1.368276560965.08089335805-0.298476491160.526656248368-0.163430845529-0.681730931630.269796808153-0.101825964662-0.3964327623410.1822834483630.05607750808040.31819586688-0.11367810190.0293641165220.23887894827-0.008611850459840.14345336072910.692114893225.8350504382-10.6908024877
71.86337707870.373208072463-2.061723618984.015627230691.479845014485.08944538774-0.1269895829690.1018818172370.142694183533-0.06131204647590.003250143127370.164329723153-0.393335718105-0.2926442137610.09671661768840.1628489654970.00162283223648-0.0272083235810.1016222483850.02597302118790.1295880416462.1880283112227.70151437436.01866703132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 60 )
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 72 )
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 95 )
6X-RAY DIFFRACTION6chain 'A' and (resid 96 through 105 )
7X-RAY DIFFRACTION7chain 'A' and (resid 106 through 125 )

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