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- PDB-6frg: Crystal structure of G-1F mutant of Ssp DnaB Mini-Intein variant M86 -

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Basic information

Entry
Database: PDB / ID: 6frg
TitleCrystal structure of G-1F mutant of Ssp DnaB Mini-Intein variant M86
ComponentsReplicative DNA helicase
KeywordsSPLICING / intein / protein splicing / Hint domain fold / pre-splicing form
Function / homology
Function and homology information


primosome complex / intein-mediated protein splicing / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / endonuclease activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding / cytosol
Similarity search - Function
Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / LAGLIDADG-like domain / DNA helicase, DnaB-like, C-terminal ...Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / LAGLIDADG-like domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Replicative DNA helicase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.535 Å
AuthorsPopp, M.A. / Blankenfeldt, W. / Friedel, K. / Mootz, H.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationMO1073/3-2 Germany
CitationJournal: Chem Sci / Year: 2019
Title: A functional interplay between intein and extein sequences in protein splicing compensates for the essential block B histidine.
Authors: Friedel, K. / Popp, M.A. / Matern, J.C.J. / Gazdag, E.M. / Thiel, I.V. / Volkmann, G. / Blankenfeldt, W. / Mootz, H.D.
History
DepositionFeb 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 20, 2019Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jan 17, 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: Replicative DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0288
Polymers18,9771
Non-polymers1,0517
Water3,981221
1
A: Replicative DNA helicase
hetero molecules

A: Replicative DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,05616
Polymers37,9542
Non-polymers2,10214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+3/21
Buried area4040 Å2
ΔGint2 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.472, 71.472, 87.871
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

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Components

#1: Protein Replicative DNA helicase


Mass: 18976.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: dnaB, slr0833 / Production host: Escherichia coli (E. coli) / References: UniProt: Q55418, DNA helicase
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3 / Details: 0.1 M sodium citrate pH 5.3, 48 % PEG200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.535→43.94 Å / Num. obs: 34745 / % possible obs: 100 % / Redundancy: 15.8 % / Biso Wilson estimate: 20.92 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.017 / Rrim(I) all: 0.068 / Net I/σ(I): 24.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.535-1.5616.31.64816830.6460.4181.701100
8.41-43.9412.80.02427410.0070.02599.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.17data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
Coot0.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MI8

1mi8


Resolution: 1.535→43.935 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.27
RfactorNum. reflection% reflection
Rfree0.1701 1735 5 %
Rwork0.1428 --
obs0.1442 34716 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.03 Å2 / Biso mean: 31.7272 Å2 / Biso min: 14.59 Å2
Refinement stepCycle: final / Resolution: 1.535→43.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1247 0 167 221 1635
Biso mean--71.92 44.48 -
Num. residues----158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181385
X-RAY DIFFRACTIONf_angle_d1.6691856
X-RAY DIFFRACTIONf_chiral_restr0.086214
X-RAY DIFFRACTIONf_plane_restr0.01225
X-RAY DIFFRACTIONf_dihedral_angle_d17.495863
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.535-1.58020.2161380.213726972835
1.5802-1.63120.23991400.210827142854
1.6312-1.68950.21491400.194326842824
1.6895-1.75710.20791490.179126952844
1.7571-1.83710.19151270.15727362863
1.8371-1.9340.17041490.141727082857
1.934-2.05510.171530.132927122865
2.0551-2.21380.16661690.130427002869
2.2138-2.43660.1461380.12527612899
2.4366-2.78910.15321390.130827762915
2.7891-3.51370.1631320.138328282960
3.5137-43.95350.17071610.142129703131
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)
12.227-0.2938-0.25541.7345-0.19871.88470.04950.1185-0.05380.00050.008-0.1848-0.01590.1348-0.06480.14930.0086-0.02240.2076-0.01410.201225.597427.351941.5342
23.14431.8589-2.56872.5945-2.61962.95330.0693-0.1072-0.4082-0.22530.0511-0.08270.81270.1279-0.02240.29620.0096-0.09080.20770.00730.310526.96314.382948.9269
35.4891-0.2855-0.0350.6174-0.27953.56280.14760.5965-0.0132-0.1115-0.01690.01530.0374-0.1579-0.10550.18330.0152-0.03290.1726-0.01630.191513.720625.588435.2184
41.9343-0.3030.55710.59870.0741.83480.1113-0.0339-0.29030.0266-0.0620.02580.1535-0.1354-0.0460.1904-0.0086-0.04960.22290.00690.22859.58718.816445.6736
53.8530.03633.6628-0.00190.03033.47350.08920.2294-0.0565-0.05880.05550.12880.12730.3796-0.10470.2429-0.0203-0.02680.27450.05690.206226.411119.96767.7536
62.806-0.0326-0.10440.7832-0.32331.93710.02930.0982-0.1814-0.03360.0007-0.04530.1383-0.0361-0.02480.1649-0.0043-0.03830.1538-0.01480.187715.68421.838742.8031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 33 )A-1 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 46 )A34 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 61 )A47 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 96 )A62 - 96
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 117 )A97 - 117
6X-RAY DIFFRACTION6chain 'A' and (resid 118 through 156 )A118 - 156

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