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- PDB-6qaz: Crystal structure of gp41-1 intein -

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Basic information

Entry
Database: PDB / ID: 6qaz
TitleCrystal structure of gp41-1 intein
Componentscyanophage-like gp41-1 intein
KeywordsUNKNOWN FUNCTION / Intein / Protein-splicing / Metagenomic
Function / homologyCITRATE ANION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsMikula, K.M. / Beyer, H.M. / Li, M. / Wlodawer, A. / Iwai, H.
Funding support Finland, United States, 4items
OrganizationGrant numberCountry
Academy of Finland137995, 277335 Finland
Novo Nordisk FoundationNNF17OC0025402 Finland
Sigrid Juselius Foundation Finland
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
CitationJournal: Febs J. / Year: 2020
Title: The crystal structure of the naturally split gp41-1 intein guides the engineering of orthogonal split inteins from cis-splicing inteins.
Authors: Beyer, H.M. / Mikula, K.M. / Li, M. / Wlodawer, A. / Iwai, H.
History
DepositionDec 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cyanophage-like gp41-1 intein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2307
Polymers14,3781
Non-polymers8526
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint9 kcal/mol
Surface area6260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.809, 69.986, 71.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-383-

HOH

21A-512-

HOH

31A-519-

HOH

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Components

#1: Protein cyanophage-like gp41-1 intein


Mass: 14378.489 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: citric acid, magnesium sulfate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.02→49.92 Å / Num. obs: 57411 / % possible obs: 92.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.019 / Net I/σ(I): 31.5
Reflection shellResolution: 1.02→1.04 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KL5

4kl5


Resolution: 1.02→49.92 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.581 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.026 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1498 2642 4.7 %RANDOM
Rwork0.1212 ---
obs0.12263 53080 89.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.477 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0 Å2
2--0.11 Å20 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.02→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 0 51 220 1275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0131157
X-RAY DIFFRACTIONr_bond_other_d0.0090.0171145
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.6491547
X-RAY DIFFRACTIONr_angle_other_deg1.5521.5962717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.155139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89727.25551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34715254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.366151
X-RAY DIFFRACTIONr_chiral_restr0.1180.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021208
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02176
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9841.603533
X-RAY DIFFRACTIONr_mcbond_other0.9841.603532
X-RAY DIFFRACTIONr_mcangle_it1.1952.425670
X-RAY DIFFRACTIONr_mcangle_other1.1942.425671
X-RAY DIFFRACTIONr_scbond_it4.0112.04623
X-RAY DIFFRACTIONr_scbond_other4.0082.04624
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5432.875873
X-RAY DIFFRACTIONr_long_range_B_refined5.523.8241336
X-RAY DIFFRACTIONr_long_range_B_other5.50123.8141336
X-RAY DIFFRACTIONr_rigid_bond_restr5.07532301
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.02→1.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 55 -
Rwork0.304 1339 -
obs--30.49 %

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