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- PDB-6rix: Crystal structure of MchDnaB-1 intein -

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Basic information

Entry
Database: PDB / ID: 6rix
TitleCrystal structure of MchDnaB-1 intein
Components(Replicative DNA helicase) x 2
KeywordsHYDROLASE / intein / protein-splicing / SPLICING
Function / homology
Function and homology information


primosome complex / intein-mediated protein splicing / DNA replication, synthesis of primer / DNA helicase activity / endonuclease activity / DNA helicase / DNA binding / ATP binding
Similarity search - Function
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 ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replicative DNA helicase
Similarity search - Component
Biological speciesMycobacterium chimaera (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.655 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 1.0May 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicative DNA helicase
B: Replicative DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1853
Polymers30,1502
Non-polymers351
Water3,963220
1
A: Replicative DNA helicase


Theoretical massNumber of molelcules
Total (without water)15,0831
Polymers15,0831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replicative DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1022
Polymers15,0671
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.246, 95.344, 35.796
Angle α, β, γ (deg.)90.000, 107.140, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Replicative DNA helicase


Mass: 15083.017 Da / Num. of mol.: 1 / Mutation: C1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium chimaera (bacteria) / Gene: BWK49_00400, MYCOZU1_00080 / Plasmid: pHBRSF073 / Production host: Escherichia coli (E. coli) / Variant (production host): T7 Express / References: UniProt: A0A220Y4A5, DNA helicase
#2: Protein Replicative DNA helicase


Mass: 15067.017 Da / Num. of mol.: 1 / Mutation: C1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium chimaera (bacteria) / Gene: BWK49_00400, MYCOZU1_00080 / Plasmid: pHBRSF073 / Production host: Escherichia coli (E. coli) / Variant (production host): T7 Express / References: UniProt: A0A220Y4A5, DNA helicase
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 % sol: 27.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Tris-HCl pH 9, magnesium chloride, polyethylene glycol 4000

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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 PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.655→50 Å / Num. obs: 22641 / % possible obs: 95 % / Redundancy: 6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.085 / Net I/σ(I): 18.7
Reflection shellResolution: 1.655→1.68 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.367 / Num. unique obs: 731 / CC1/2: 0.543 / % possible all: 60.2

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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: 6BS8

6bs8


Resolution: 1.655→47.672 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 20.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1037 4.82 %
Rwork0.1586 20484 -
obs0.1612 21521 90.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.79 Å2 / Biso mean: 18.4114 Å2 / Biso min: 3.46 Å2
Refinement stepCycle: final / Resolution: 1.655→47.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 1 220 2132
Biso mean--17.35 32.96 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591999
X-RAY DIFFRACTIONf_angle_d0.84742751
X-RAY DIFFRACTIONf_chiral_restr0.0565330
X-RAY DIFFRACTIONf_plane_restr0.0055363
X-RAY DIFFRACTIONf_dihedral_angle_d2.53151594
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6555-1.74280.2973780.2278145345
1.7428-1.8520.24421600.204283389
1.852-1.9950.20961700.1675322799
1.995-2.19570.2181400.1508320299
2.1957-2.51340.2011750.15493223100
2.5134-3.16660.20381380.16473280100
3.1666-47.60.20751760.143266100
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)
12.2396-0.3304-0.10121.7745-0.36352.61480.1311-0.2050.13590.1848-0.01760.0314-0.15850.0109-0.10390.0545-0.02210.01160.0585-0.00090.0631-3.595913.341217.1909
25.36010.1385-1.26630.9854-0.35793.15390.0022-0.4154-0.12420.139-0.04150.01550.02290.13080.02880.1051-0.0084-0.00670.02580.00820.0609-1.55166.065919.4477
37.725-0.91923.37892.5122-0.98643.1892-0.10110.29790.194-0.25430.03740.12-0.194-0.09610.04660.09460.0204-0.01740.1295-0.00670.0801-2.0796.38111.783
41.5882-0.068-0.25783.9108-0.42732.02930.04280.1738-0.2253-0.0645-0.0687-0.32840.18330.07580.03340.08330.0229-0.00480.0503-0.01370.1013-0.2059-1.74597.4351
55.6373-0.7666-4.58957.33890.80627.4326-0.19790.3802-0.288-0.6723-0.03240.11120.5659-0.26190.23350.18530.009-0.0070.1789-0.01870.1133-6.9403-3.38391.675
63.51480.10060.59421.2620.61322.8899-0.04670.2576-0.1385-0.0851-0.01160.11080.0924-0.00730.03180.09130.00720.00060.07090.02260.0847-0.94653.65046.1057
76.07774.9006-0.77077.1965-0.40644.17350.0945-0.287-0.49950.3222-0.2021-0.01330.8155-0.0670.0950.2556-0.02760.02240.12780.03980.1728-6.3889-0.465222.0525
86.03640.8779-0.52235.74410.86054.93520.0248-0.0624-0.0606-0.031-0.0416-0.02630.22840.006-0.01870.05790.00190.01010.03830.00440.0579-7.35644.722112.2489
93.69450.63320.14742.67890.17982.57450.1487-0.12710.01550.226-0.0545-0.1761-0.14720.1348-0.05660.0791-0.00770.00590.0550.01270.0688-0.564625.556713.1653
103.37030.9387-0.81722.07410.85122.13830.1044-0.27430.53830.0636-0.16170.4262-0.2841-0.22740.10270.11270.00890.02920.10550.02080.1237-9.896530.867112.0898
113.5053-3.3906-1.9144.43261.77991.4298-0.23590.0592-0.3953-0.08970.1580.08160.1756-0.00270.06790.1221-0.00330.00620.13010.00670.0812-4.054220.125-2.7158
124.30082.6421-1.36824.2679-2.36662.01970.03760.19990.2295-0.22790.14720.2594-0.0534-0.165-0.17080.10190.01310.02460.07430.01860.086-5.888929.8187-2.973
138.12751.11444.03028.17783.34743.3169-0.27571.0204-0.1765-0.31710.2315-0.3443-0.41230.97950.02010.2365-0.02520.03220.30150.02520.16562.364329.0192-8.3061
145.2406-0.1902-0.99891.78950.45782.8692-0.01710.464-0.0255-0.1851-0.02360.00670.1024-0.03480.03510.0865-0.0079-0.02250.05310.02240.0755-6.516823.7077-1.1511
156.82546.296-3.98927.5774-3.06316.38110.05940.00370.4646-0.0011-0.04490.5915-0.43590.0361-0.02130.2228-0.0203-0.00060.0646-0.02720.1787-0.552137.579.7705
163.68322.22120.75655.4644-0.5345.9687-0.00620.00990.2008-0.0062-0.04490.1174-0.2592-0.05630.02780.04050.00040.01370.0557-0.00090.06980.751327.8884.7937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 47 )A25 - 47
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 57 )A48 - 57
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 78 )A58 - 78
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 88 )A79 - 88
6X-RAY DIFFRACTION6chain 'A' and (resid 89 through 124 )A89 - 124
7X-RAY DIFFRACTION7chain 'A' and (resid 125 through 132 )A125 - 132
8X-RAY DIFFRACTION8chain 'A' and (resid 133 through 145 )A133 - 145
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 32 )B1 - 32
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 47 )B33 - 47
11X-RAY DIFFRACTION11chain 'B' and (resid 48 through 57 )B48 - 57
12X-RAY DIFFRACTION12chain 'B' and (resid 58 through 78 )B58 - 78
13X-RAY DIFFRACTION13chain 'B' and (resid 79 through 105 )B79 - 105
14X-RAY DIFFRACTION14chain 'B' and (resid 106 through 124 )B106 - 124
15X-RAY DIFFRACTION15chain 'B' and (resid 125 through 132 )B125 - 132
16X-RAY DIFFRACTION16chain 'B' and (resid 133 through 145 )B133 - 145

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