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- PDB-4nl4: PriA Helicase Bound to ADP -

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Basic information

Entry
Database: PDB / ID: 4nl4
TitlePriA Helicase Bound to ADP
ComponentsPrimosome assembly protein PriA
KeywordsDNA BINDING PROTEIN / RecA / PriA / winged-helix / 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 / hydrolase activity / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
PriA, 3(prime) DNA-binding 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, 3(prime) DNA-binding 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 / GIY-YIG endonuclease / 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 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Primosomal protein N'
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsBhattacharyya, B. / George, N.P. / 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 1.2May 27, 2015Group: Refinement description
Revision 1.3Feb 28, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
H: Primosome assembly protein PriA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7954
Polymers83,2371
Non-polymers5583
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.433, 85.433, 111.682
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Primosome assembly protein PriA


Mass: 83237.211 Da / Num. of mol.: 1
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: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: A6TGC5
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 mM Tris-HCl, pH 8.0, 5% MPD, 6% PEG 6000, 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-D / Wavelength: 1.008 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2011 / Details: Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 26617 / Num. obs: 26617 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.072 / Net I/σ(I): 23.78
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.34 / Rsym value: 0.838 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.65→35.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 24.056 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 0.789 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25401 1342 5 %RANDOM
Rwork0.21763 ---
obs0.21957 25249 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.927 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.08 Å2-0 Å2
2--0.08 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.65→35.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5485 0 29 28 5542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195659
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.9597700
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.735694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28223.206262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73315919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0141549
X-RAY DIFFRACTIONr_chiral_restr0.0590.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214316
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.646→2.715 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 92 -
Rwork0.315 1860 -
obs--100 %
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)
12.9324-1.5867-1.01492.73061.25723.1979-0.2841-0.2418-0.54040.28670.09880.07980.60950.2580.18530.24790.15160.0960.12340.07470.236333.0031-42.1928-12.0412
22.5095-0.19590.30193.26380.31622.45840.06550.62160.177-1.099-0.2223-0.066-0.14020.18320.15680.50850.18670.05930.36760.0380.257930.6483-16.9726-43.191
32.0437-0.3036-0.77262.17050.02461.5313-0.0015-0.20430.12950.0656-0.03590.11110.00650.13370.03750.03830.0289-0.03470.1339-0.04030.120924.7844-14.3447-8.2918
42.67390.3796-0.18940.6673-0.34942.2217-0.16190.29680.54-0.05230.34230.1785-0.3365-0.3877-0.18040.19460.03780.0050.21440.10310.2503-6.8543-6.6255-6.6034
59.56150.1756-1.84377.1123-1.23814.7746-0.43320.6445-1.3123-0.1798-0.1838-0.28090.6218-0.04910.6170.1258-0.02790.14440.177-0.02920.2895-14.2964-28.48165.7439
600000000000000-00.1394000.139400.1394000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 105
2X-RAY DIFFRACTION2H106 - 197
3X-RAY DIFFRACTION3H198 - 371
4X-RAY DIFFRACTION4H372 - 430
5X-RAY DIFFRACTION5H431 - 487
6X-RAY DIFFRACTION6H630 - 720

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