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- PDB-6frh: Crystal structure of Ssp DnaB Mini-Intein variant M86 -

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Basic information

Entry
Database: PDB / ID: 6frh
TitleCrystal structure of Ssp DnaB Mini-Intein variant M86
ComponentsReplicative DNA helicase,Replicative DNA helicase
KeywordsSPLICING / intein / protein splicing / Hint domain fold / pre-splicing
Function / homology
Function and homology information


primosome complex / DNA 5'-3' helicase / intein-mediated protein splicing / DNA replication, synthesis of primer / DNA helicase activity / isomerase activity / endonuclease activity / Hydrolases; Acting on ester bonds / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity ...primosome complex / DNA 5'-3' helicase / intein-mediated protein splicing / DNA replication, synthesis of primer / DNA helicase activity / isomerase activity / endonuclease activity / Hydrolases; Acting on ester bonds / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication / 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 / LAGLIDADG-like domain / DnaB-like helicase C terminal 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 / LAGLIDADG-like domain / DnaB-like helicase C terminal 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. / Homing endonuclease / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Replicative DNA helicase DnaB
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
AuthorsPopp, M.A. / Blankenfeldt, W. / Gazdag, M.E. / Matern, J.J.C. / 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 ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
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 / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Feb 20, 2019Group: Data collection / Structure summary / Category: audit_author / pdbx_seq_map_depositor_info
Item: _audit_author.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicative DNA helicase,Replicative DNA helicase
B: Replicative DNA helicase,Replicative DNA helicase


Theoretical massNumber of molelcules
Total (without water)37,7742
Polymers37,7742
Non-polymers00
Water3,189177
1
A: Replicative DNA helicase,Replicative DNA helicase


Theoretical massNumber of molelcules
Total (without water)18,8871
Polymers18,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replicative DNA helicase,Replicative DNA helicase


Theoretical massNumber of molelcules
Total (without water)18,8871
Polymers18,8871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.635, 40.941, 57.906
Angle α, β, γ (deg.)84.370, 83.450, 65.000
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -5 through 35 or resid 37...
21(chain B and (resid -5 through 34 or (resid 35...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLUGLU(chain A and (resid -5 through 35 or resid 37...AA-5 - 352 - 41
12THRTHRALAALA(chain A and (resid -5 through 35 or resid 37...AA37 - 4343 - 49
13LYSLYSLYSLYS(chain A and (resid -5 through 35 or resid 37...AA4450
14LEULEULYSLYS(chain A and (resid -5 through 35 or resid 37...AA-5 - 1602 - 166
15LEULEULYSLYS(chain A and (resid -5 through 35 or resid 37...AA-5 - 1602 - 166
16LEULEULYSLYS(chain A and (resid -5 through 35 or resid 37...AA-5 - 1602 - 166
17LEULEULYSLYS(chain A and (resid -5 through 35 or resid 37...AA-5 - 1602 - 166
21LEULEUASNASN(chain B and (resid -5 through 34 or (resid 35...BB-5 - 342 - 40
22GLUGLUGLUGLU(chain B and (resid -5 through 34 or (resid 35...BB3541
23LEULEUGLNGLN(chain B and (resid -5 through 34 or (resid 35...BB-5 - 1582 - 164
24LEULEUGLNGLN(chain B and (resid -5 through 34 or (resid 35...BB-5 - 1582 - 164
25LEULEUGLNGLN(chain B and (resid -5 through 34 or (resid 35...BB-5 - 1582 - 164
26LEULEUGLNGLN(chain B and (resid -5 through 34 or (resid 35...BB-5 - 1582 - 164

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Components

#1: Protein Replicative DNA helicase,Replicative DNA helicase


Mass: 18886.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria), (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 1.95 Å3/Da / Density % sol: 37.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.1 M Tris pH 7.6, 22 % PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.03→37.05 Å / Num. obs: 18028 / % possible obs: 96.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.22 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.098 / Rrim(I) all: 0.183 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.03-2.083.50.75713290.7060.4750.89796.2
9.06-37.053.60.0862050.9910.0520.10198.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIXdev_2733refinement
PDB_EXTRACT3.24data extraction
Coot0.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MI8

1mi8


Resolution: 2.03→31.951 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.94
RfactorNum. reflection% reflection
Rfree0.2417 882 4.93 %
Rwork0.2218 --
obs0.2228 17875 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.35 Å2 / Biso mean: 35.3813 Å2 / Biso min: 9.39 Å2
Refinement stepCycle: final / Resolution: 2.03→31.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 0 177 2555
Biso mean---34.96 -
Num. residues----310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022435
X-RAY DIFFRACTIONf_angle_d0.4923306
X-RAY DIFFRACTIONf_chiral_restr0.045398
X-RAY DIFFRACTIONf_plane_restr0.002416
X-RAY DIFFRACTIONf_dihedral_angle_d13.4091478
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1706X-RAY DIFFRACTION6.848TORSIONAL
12B1706X-RAY DIFFRACTION6.848TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.15720.32211360.29132836297296
2.1572-2.32370.27861640.26642804296897
2.3237-2.55750.26881270.24142864299196
2.5575-2.92730.26621540.23222831298597
2.9273-3.68720.21321540.20462815296997
3.6872-31.95520.21541470.19232843299097
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)
10.02140.0002-0.02960.0384-0.02180.02630.0165-0.0734-0.164-0.0036-0.0930.00880.01660.0532-00.12860.0110.0110.1657-0.00950.2192.744813.1518-22.2811
20.1276-0.0428-0.09870.04690.00270.10550.1013-0.01530.03560.06740.0303-0.1099-0.0407-0.12430.02180.1099-0.0326-0.01140.1492-0.02070.12882.900917.2172-22.6037
30.0261-0.00770.0250.01840.01050.0301-0.0954-0.00120.0213-0.1139-0.0458-0.02490.1001-0.0483-00.16520.00880.02430.16090.00650.21240.44490.0329-9.484
40.228-0.00980.0290.018-0.10230.5468-0.2468-0.27680.39330.15250.0761-0.1805-0.4009-0.05910.00820.1821-0.0101-0.04440.2296-0.05620.26251.64169.29783.8642
50.03910.0266-0.00270.04790.03210.37180.091-0.06940.3314-0.0551-0.00790.12390.1211-0.1350.00740.1583-0.03-0.01580.1370.00970.2491-5.7731.0224-8.5138
60.07370.01620.12540.2391-0.20240.41060.0494-0.1415-0.0537-0.1924-0.0588-0.0520.4428-0.04130.0070.1804-0.01140.02950.1464-0.00640.15482.046-8.4398-0.5027
7-0.0003-0.0015-0.00230.00280.00620.0136-0.13540.06890.04470.12450.0150.0078-0.0020.189100.5246-0.04630.01280.4639-0.13040.37673.4736-1.237117.5958
80.08610.0189-0.10590.10760.05150.1684-0.0592-0.18890.06380.041-0.01050.10120.1235-0.1314-0.05240.2501-0.0493-0.03670.18160.03520.1662-3.9912-8.66460.299
90.0637-0.07580.03270.0743-0.04180.0224-0.0239-0.0480.1037-0.0090.0412-0.01730.0116-0.01720.00530.1127-0.0357-0.00820.13360.00450.25343.51064.5587-3.9864
100.1966-0.0196-0.23510.00720.03280.27510.03530.12770.02140.10450.0369-0.1732-0.1648-0.13230.02450.2055-0.0261-0.06440.15060.00190.20150.429719.1733-15.8137
110.46470.0851-0.30010.0623-0.11650.3392-0.23540.0948-0.4906-0.1136-0.18650.05350.45720.0685-0.25540.1699-0.02370.04760.2471-0.08430.2693-2.3728.5108-28.4172
120.0156-0.0029-0.01010.0138-0.01020.0049-0.09170.1408-0.32230.0654-0.00030.06170.12140.30.00010.1612-0.03270.03830.3015-0.03220.208211.364413.6855-30.7934
130.06430.01910.03710.10420.16040.22570.0014-0.0298-0.03410.0143-0.10720.10460.0229-0.0769-0.02570.1668-0.00060.020.10770.00780.1561-5.625218.6202-17.4147
140.29930.01710.11920.17970.03040.05020.37630.28140.1128-0.2171-0.07370.0231-0.0564-0.1690.2120.10720.312-0.1316-0.08180.2333-0.0523-3.673725.7198-25.8776
150.0429-0.0107-0.03210.0294-0.02430.05630.20960.08020.1248-0.0004-0.2224-0.262-0.46110.0365-0.00160.2552-0.0170.01990.22250.01940.16755.120128.4713-24.3045
160.01370.0139-0.01410.0189-0.00550.05360.0123-0.0205-0.00460.05680.04250.00730.0682-0.08420.07760.47350.15370.08870.3465-0.01960.089813.594420.5337-41.7489
170.02010.03370.02190.12670.03890.51390.13530.13040.0455-0.2206-0.12790.1062-0.1691-0.273-0.09530.27330.0630.06130.17420.0440.1192-4.083427.899-25.748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 134 through 147 )B134 - 147
2X-RAY DIFFRACTION2chain 'B' and (resid 148 through 158 )B148 - 158
3X-RAY DIFFRACTION3chain 'A' and (resid -5 through 6 )A-5 - 6
4X-RAY DIFFRACTION4chain 'A' and (resid 7 through 45 )A7 - 45
5X-RAY DIFFRACTION5chain 'A' and (resid 46 through 60 )A46 - 60
6X-RAY DIFFRACTION6chain 'A' and (resid 61 through 96 )A61 - 96
7X-RAY DIFFRACTION7chain 'A' and (resid 97 through 117 )A97 - 117
8X-RAY DIFFRACTION8chain 'A' and (resid 118 through 133 )A118 - 133
9X-RAY DIFFRACTION9chain 'A' and (resid 134 through 160 )A134 - 160
10X-RAY DIFFRACTION10chain 'B' and (resid -5 through 6 )B-5 - 6
11X-RAY DIFFRACTION11chain 'B' and (resid 7 through 34 )B7 - 34
12X-RAY DIFFRACTION12chain 'B' and (resid 35 through 45 )B35 - 45
13X-RAY DIFFRACTION13chain 'B' and (resid 46 through 60 )B46 - 60
14X-RAY DIFFRACTION14chain 'B' and (resid 61 through 73 )B61 - 73
15X-RAY DIFFRACTION15chain 'B' and (resid 74 through 96 )B74 - 96
16X-RAY DIFFRACTION16chain 'B' and (resid 97 through 117 )B97 - 117
17X-RAY DIFFRACTION17chain 'B' and (resid 118 through 133 )B118 - 133

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