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- PDB-6blb: 1.88 Angstrom Resolution Crystal Structure Holliday Junction ATP-... -

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Basic information

Entry
Database: PDB / ID: 6blb
Title1.88 Angstrom Resolution Crystal Structure Holliday Junction ATP-dependent DNA Helicase (RuvB) from Pseudomonas aeruginosa in Complex with ADP
ComponentsHolliday junction ATP-dependent DNA helicase RuvB
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Holliday Junction ATP-dependent DNA Helicase / ADP
Function / homology
Function and homology information


cellular response to chromate / cellular response to selenite ion / Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA recombination / DNA repair / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / RuvB-like P-loop domain / RuvB, AAA lid domain / RuvB C-terminal winged helix domain / Holliday junction DNA helicase RuvB P-loop domain / RuvB AAA lid domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / RuvB-like P-loop domain / RuvB, AAA lid domain / RuvB C-terminal winged helix domain / Holliday junction DNA helicase RuvB P-loop domain / RuvB AAA lid domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / ATPase family associated with various cellular activities (AAA) / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TRIETHYLENE GLYCOL / Holliday junction branch migration complex subunit RuvB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionNov 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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
Revision 1.2Jun 18, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Holliday junction ATP-dependent DNA helicase RuvB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8313
Polymers39,2541
Non-polymers5772
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, 1IN4
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-2 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.537, 85.537, 77.103
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Holliday junction ATP-dependent DNA helicase RuvB / Holliday Junction ATP-dependent DNA Helicase


Mass: 39253.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ruvB, PA0967 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q51426, DNA helicase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 8.6 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris, pH 8.3, screen: Classics II (D3), 0.1 M HEPES, pH 7.0, 30% v/v Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2017 / Details: C(111)
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 26154 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.028 / Rrim(I) all: 0.081 / Rsym value: 0.076 / Χ2: 1.01 / Net I/σ(I): 26.9
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1311 / CC1/2: 0.811 / Rpim(I) all: 0.291 / Rrim(I) all: 0.849 / Rsym value: 0.797 / Χ2: 1.009 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IN4

1in4


Resolution: 1.88→28.64 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.796 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.136 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21307 1295 5 %RANDOM
Rwork0.17247 ---
obs0.17452 24830 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.916 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.88→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 37 191 2658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192601
X-RAY DIFFRACTIONr_bond_other_d0.0010.022528
X-RAY DIFFRACTIONr_angle_refined_deg1.3692.0043533
X-RAY DIFFRACTIONr_angle_other_deg0.86835825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9645327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.49922.479121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69715456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.191533
X-RAY DIFFRACTIONr_chiral_restr0.0810.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.0212907
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02541
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_it1.2092.1741287
X-RAY DIFFRACTIONr_mcbond_other1.2082.171286
X-RAY DIFFRACTIONr_mcangle_it1.8523.2471621
X-RAY DIFFRACTIONr_mcangle_other1.8513.2511622
X-RAY DIFFRACTIONr_scbond_it1.8472.5541314
X-RAY DIFFRACTIONr_scbond_other1.8462.5541314
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0083.7231913
X-RAY DIFFRACTIONr_long_range_B_refined5.27926.9912894
X-RAY DIFFRACTIONr_long_range_B_other5.13726.7062864
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 104 -
Rwork0.222 1827 -
obs--99.69 %
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)
12.674-2.8089-0.32194.87270.86571.51230.08760.21850.3029-0.2869-0.1113-0.2511-0.1861-0.08650.02370.04340.00670.01330.03510.03830.082638.854510.4006-3.5734
22.4357-0.2345-0.1674.4860.54581.38310.06740.2771-0.1119-0.3737-0.1280.598-0.0315-0.07660.06060.04650.0189-0.06510.0487-0.01860.103623.6992-1.9655-8.3494
37.75460.40752.83366.06190.23011.54710.286-1.19630.07290.7967-0.34070.65230.2399-0.34110.05480.1433-0.05520.09720.217-0.03460.102223.3856-0.04554.3029
40.75930.0425-0.20253.2315-1.74961.9947-0.0184-0.03560.05250.063-0.1254-0.1870.02680.15220.14380.01590.0078-0.0130.01980.00850.033226.789132.4637-1.7248
54.16291.2332-0.67792.5136-0.70332.3716-0.00350.2415-0.0737-0.16820.13930.18940.0813-0.1803-0.13580.0165-0.001-0.0220.0415-0.00150.03178.583621.51459.3162
61.66241.33160.26056.25411.03860.44410.1517-0.29030.06330.1378-0.1650.0482-0.0321-0.12390.01330.0279-0.00740.00190.0811-0.01140.00928.387424.514321.1205
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 54
2X-RAY DIFFRACTION2A55 - 161
3X-RAY DIFFRACTION3A162 - 180
4X-RAY DIFFRACTION4A181 - 258
5X-RAY DIFFRACTION5A259 - 313
6X-RAY DIFFRACTION6A314 - 338

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