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- PDB-5v9x: Structure of Mycobacterium smegmatis helicase Lhr bound to ssDNA ... -

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Basic information

Entry
Database: PDB / ID: 5v9x
TitleStructure of Mycobacterium smegmatis helicase Lhr bound to ssDNA and AMP-PNP
Components
  • ATP-dependent DNA helicase
  • ssDNA
KeywordsHYDROLASE/DNA / Helicase / HYDROLASE-DNA complex
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / helicase activity / nucleic acid binding / RNA helicase activity / RNA helicase / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
: / DEAD/H associated / DEAD/H associated / DNA glycosylase AlkZ-like / DNA glycosylase AlkZ-like / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...: / DEAD/H associated / DEAD/H associated / DNA glycosylase AlkZ-like / DNA glycosylase AlkZ-like / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / ATP-dependent DNA helicase / DEAD/DEAH box helicase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.797 Å
AuthorsOrdonez, H. / Jacewicz, A. / Ferrao, R. / Shuman, S.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structure of mycobacterial 3'-to-5' RNA:DNA helicase Lhr bound to a ssDNA tracking strand highlights distinctive features of a novel family of bacterial helicases.
Authors: Ejaz, A. / Ordonez, H. / Jacewicz, A. / Ferrao, R. / Shuman, S.
History
DepositionMar 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent DNA helicase
B: ssDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0019
Polymers99,9962
Non-polymers1,0057
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-35 kcal/mol
Surface area31520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.462, 88.129, 83.675
Angle α, β, γ (deg.)90.00, 109.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / DNA chain , 2 types, 2 molecules AB

#1: Protein ATP-dependent DNA helicase


Mass: 95065.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: lhr, ERS451418_01790 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6HFY2, UniProt: A0QT91*PLUS, RNA helicase
#2: DNA chain ssDNA


Mass: 4930.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Non-polymers , 5 types, 25 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 21 - 22 % (w/v) PEG3350, 0.2 M NaF, 0.1 M Bis-Tris Propane (pH 7.0 - 7.2)
PH range: 7.0-7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.797→99 Å / Num. obs: 25197 / % possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 15.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.797→45.755 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.04
RfactorNum. reflection% reflection
Rfree0.2424 1998 7.97 %
Rwork0.1953 --
obs0.1991 25069 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.797→45.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5897 271 63 18 6249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036374
X-RAY DIFFRACTIONf_angle_d0.6098728
X-RAY DIFFRACTIONf_dihedral_angle_d16.6082379
X-RAY DIFFRACTIONf_chiral_restr0.0441012
X-RAY DIFFRACTIONf_plane_restr0.0041094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.797-2.86690.32731240.28561431X-RAY DIFFRACTION86
2.8669-2.94440.35531420.26021633X-RAY DIFFRACTION99
2.9444-3.03110.28241450.2511672X-RAY DIFFRACTION99
3.0311-3.12890.29611420.23071646X-RAY DIFFRACTION100
3.1289-3.24070.33141440.23561658X-RAY DIFFRACTION99
3.2407-3.37040.26011430.22771657X-RAY DIFFRACTION99
3.3704-3.52370.28091430.21651647X-RAY DIFFRACTION99
3.5237-3.70940.2711420.19241648X-RAY DIFFRACTION100
3.7094-3.94170.22791490.18371708X-RAY DIFFRACTION100
3.9417-4.24590.20471420.17241642X-RAY DIFFRACTION99
4.2459-4.67280.21651440.15581655X-RAY DIFFRACTION99
4.6728-5.3480.20991450.17181672X-RAY DIFFRACTION100
5.348-6.73450.26771460.21685X-RAY DIFFRACTION99
6.7345-45.76090.19861470.18581717X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.2591-0.28060.27211.0475-0.17261.31720.0013-0.0963-0.00580.0134-0.06810.0516-0.012-0.06030.06630.3966-0.02010.04920.3702-0.00270.293218.9521-18.65214.8211
20.6673-0.6060.20261.10660.36030.6323-0.0275-0.041-0.0752-0.01540.005-0.23890.40110.0950.02180.66330.06880.01260.56860.08130.513738.0805-39.265417.3899
31.1856-0.37850.44314.1145-0.37441.31520.0256-0.2160.00410.0438-0.1012-0.41910.02060.30740.09060.48490.0088-0.00990.62890.12790.393846.3648-30.804627.9642
44.786-2.9721-0.89944.42123.18974.6875-0.0135-0.10620.27260.3063-0.0449-1.0532-0.00230.24280.09180.4822-0.1426-0.01230.54990.09810.553234.2606-17.31839.1016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 522 )
2X-RAY DIFFRACTION2chain 'A' and (resid 523 through 655 )
3X-RAY DIFFRACTION3chain 'A' and (resid 656 through 852 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 15 )

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