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- PDB-2is4: Crystal structure of UvrD-DNA-ADPNP ternary complex -

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Basic information

Entry
Database: PDB / ID: 2is4
TitleCrystal structure of UvrD-DNA-ADPNP ternary complex
Components
  • 25-MER
  • DNA helicase II
KeywordsHYDROLASE/DNA / DNA helicase / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


rolling circle DNA replication / single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / DNA helicase complex / nucleotide-excision repair, DNA duplex unwinding / DNA translocase activity / DNA 3'-5' helicase / recombinational repair / DNA duplex unwinding / single-stranded DNA helicase activity ...rolling circle DNA replication / single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / DNA helicase complex / nucleotide-excision repair, DNA duplex unwinding / DNA translocase activity / DNA 3'-5' helicase / recombinational repair / DNA duplex unwinding / single-stranded DNA helicase activity / replication fork processing / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / SOS response / mismatch repair / DNA helicase activity / isomerase activity / nucleotide-excision repair / response to radiation / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding / cytosol
Similarity search - Function
DNA helicase, ATP-dependent, UvrD type / PcrA/UvrD tudor domain / Arc Repressor Mutant, subunit A - #160 / PCRA; domain 4 / PCRA; domain 4 / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain ...DNA helicase, ATP-dependent, UvrD type / PcrA/UvrD tudor domain / Arc Repressor Mutant, subunit A - #160 / PCRA; domain 4 / PCRA; domain 4 / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / DNA helicase II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYang, W. / Lee, J.Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke.
Authors: Lee, J.Y. / Yang, W.
History
DepositionOct 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). THE ASSYMETRIC UNIT CONTAINS TWO BIOLOGICAL UNITS. BIOLOGICAL UNIT ONE CONTAINS CHAINS A, C (RESIDUES 1-10) AND D (RESIDUES 11-26). BIOLOGICAL UNIT TWO CONTAINS CHAINS B, C (RESIDUES 11-20) AND D (RESIDUES 22-26).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 25-MER
D: 25-MER
A: DNA helicase II
B: DNA helicase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,6258
Polymers171,5644
Non-polymers1,0614
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.112, 96.779, 111.044
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 25-MER


Mass: 7985.137 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA helicase II


Mass: 77797.078 Da / Num. of mol.: 2 / Mutation: A399V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: uvrD / Production host: Escherichia coli (E. coli)
References: UniProt: P03018, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG3350, Sodium fluoride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-IDVolume (Å3)
1PEG 335011
2Sodium Fluoride11
3H2O11
4PEG 335012
5Sodium Fluoride12Fluoride'?

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 4, 2005
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 68018 / Num. obs: 61012 / % possible obs: 89.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 77.04 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3487 / % possible all: 51.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2IS1

2is1


Resolution: 2.6→29.84 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 278489.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 5887 10.2 %RANDOM
Rwork0.215 ---
obs0.215 57871 85.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.9828 Å2 / ksol: 0.305785 e/Å3
Displacement parametersBiso mean: 79 Å2
Baniso -1Baniso -2Baniso -3
1-21.11 Å20 Å29.21 Å2
2--9.58 Å20 Å2
3----30.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9951 1015 64 118 11148
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it3.082.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.395 520 9.6 %
Rwork0.348 4898 -
obs--48.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5anp.paranp.top

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