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- PDB-4nl8: PriA Helicase Bound to SSB C-terminal Tail Peptide -

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Basic information

Entry
Database: PDB / ID: 4nl8
TitlePriA Helicase Bound to SSB C-terminal Tail Peptide
Components
  • Primosome assembly protein PriA
  • Single-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / PriA / SSB C-Terminal peptide / RecA fold / winged helix domain / helicase
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / single-stranded DNA binding / DNA recombination / DNA replication / hydrolase activity / DNA repair ...primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / single-stranded DNA binding / DNA recombination / DNA replication / hydrolase activity / DNA repair / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
: / Primosomal protein N'-like, winged helix / Primosomal protein N' / PriA DNA helicase, Cys-rich region (CRR) domain / Primosomal protein N', 3' DNA-binding domain / Primosomal protein N, C-terminal domain / Primosomal protein N', 3' DNA-binding domain superfamily / 3'DNA-binding domain (3'BD) / Primosomal protein N C-terminal domain / PriA DNA helicase Cys-rich region (CRR) domain ...: / Primosomal protein N'-like, winged helix / Primosomal protein N' / PriA DNA helicase, Cys-rich region (CRR) domain / Primosomal protein N', 3' DNA-binding domain / Primosomal protein N, C-terminal domain / Primosomal protein N', 3' DNA-binding domain superfamily / 3'DNA-binding domain (3'BD) / Primosomal protein N C-terminal domain / PriA DNA helicase Cys-rich region (CRR) domain / Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Single-stranded DNA-binding protein / Primosomal protein N' / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.08 Å
AuthorsBhattacharyya, B. / George, N.P. / Thurmes, T.M. / Keck, J.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural mechanisms of PriA-mediated DNA replication restart.
Authors: Bhattacharyya, B. / George, N.P. / Thurmes, T.M. / Zhou, R. / Jani, N. / Wessel, S.R. / Sandler, S.J. / Ha, T. / Keck, J.L.
History
DepositionNov 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Single-stranded DNA-binding protein
A: Primosome assembly protein PriA
D: Single-stranded DNA-binding protein
B: Primosome assembly protein PriA
F: Single-stranded DNA-binding protein
E: Primosome assembly protein PriA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,00512
Polymers253,6136
Non-polymers3926
Water00
1
C: Single-stranded DNA-binding protein
A: Primosome assembly protein PriA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6684
Polymers84,5382
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Single-stranded DNA-binding protein
B: Primosome assembly protein PriA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6684
Polymers84,5382
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Single-stranded DNA-binding protein
E: Primosome assembly protein PriA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6684
Polymers84,5382
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.610, 153.248, 192.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13B
23E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 3 - 731 / Label seq-ID: 19 - 747

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AB
21BD
12AB
22EF
13BD
23EF

NCS ensembles :
ID
1
2
3

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Components

#1: Protein/peptide Single-stranded DNA-binding protein


Mass: 1300.392 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: HS11286 / Gene: KPHS_02830, ssb c-terminal peptide / Production host: Escherichia coli (E. coli) / References: UniProt: G8W6B0, UniProt: A0A0H3GL04*PLUS
#2: Protein Primosome assembly protein PriA


Mass: 83237.211 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: MGH 78578 / Gene: KPN78578_41850, KPN_04230, priA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: A6TGC5
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M ammonium acetate, 0.015 M magnesium acetate tetrahydrate, 0.05 M sodium cacodylate trihydrate pH 6.5, and 10% v/v 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2013 / Details: C(111)
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 4.08→50 Å / Num. obs: 21752 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.108 / Net I/σ(I): 10.91
Reflection shellResolution: 4.08→4.17 Å / Mean I/σ(I) obs: 1.89 / Rsym value: 0.495 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERMRphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.08→50 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.867 / SU B: 58.968 / SU ML: 0.776 / Cross valid method: THROUGHOUT / ESU R Free: 1.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29848 1103 5.1 %RANDOM
Rwork0.24046 ---
obs0.24341 20649 84.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 142.274 Å2
Baniso -1Baniso -2Baniso -3
1-5.13 Å20 Å2-0 Å2
2---1.02 Å2-0 Å2
3----4.11 Å2
Refinement stepCycle: LAST / Resolution: 4.08→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13359 0 6 0 13365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01913721
X-RAY DIFFRACTIONr_bond_other_d0.0040.0213306
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.95718661
X-RAY DIFFRACTIONr_angle_other_deg0.9333.00230423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99951668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15323.238627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.309152211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.70615109
X-RAY DIFFRACTIONr_chiral_restr0.0640.22106
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115394
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023247
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_it10.39713.976759
X-RAY DIFFRACTIONr_mcbond_other10.39613.9686758
X-RAY DIFFRACTIONr_mcangle_it16.78220.9248389
X-RAY DIFFRACTIONr_mcangle_other17.40422.148390
X-RAY DIFFRACTIONr_scbond_it9.31214.5426962
X-RAY DIFFRACTIONr_scbond_other9.72315.3856962
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.1322.82910269
X-RAY DIFFRACTIONr_long_range_B_refined26.47754051
X-RAY DIFFRACTIONr_long_range_B_other26.47654048
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A327880.05
12B327880.05
21A321220.07
22E321220.07
31B345150.06
32E345150.06
LS refinement shellResolution: 4.08→4.183 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 69 -
Rwork0.267 1291 -
obs--73.28 %

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