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- PDB-1q57: The Crystal Structure of the Bifunctional Primase-Helicase of Bac... -

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Entry
Database: PDB / ID: 1q57
TitleThe Crystal Structure of the Bifunctional Primase-Helicase of Bacteriophage T7
ComponentsDNA primase/helicase
KeywordsTRANSFERASE / primase / helicase / dNTPase / DNA replication
Function / homology
Function and homology information


DNA primase activity / viral DNA genome replication / DNA helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / single-stranded DNA binding / 5'-3' DNA helicase activity / DNA helicase / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
N-terminal domain of TfIIb - #180 / Bacteriophage T7 DNA helicase/primase / : / Bacteriophage T7 DNA helicase/primase, N-terminal a+b fold / Bacteriophage T7, Gp4, DNA primase/helicase, N-terminal / Zinc-binding domain of primase-helicase / Zinc-binding domain of primase-helicase / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / Twinkle-like protein ...N-terminal domain of TfIIb - #180 / Bacteriophage T7 DNA helicase/primase / : / Bacteriophage T7 DNA helicase/primase, N-terminal a+b fold / Bacteriophage T7, Gp4, DNA primase/helicase, N-terminal / Zinc-binding domain of primase-helicase / Zinc-binding domain of primase-helicase / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / Twinkle-like protein / Archaeal primase DnaG/twinkle-like, TOPRIM domain / Toprim-like / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / TOPRIM / N-terminal domain of TfIIb / Toprim domain profile. / TOPRIM domain / Single Sheet / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA helicase/primase
Similarity search - Component
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MIR / Resolution: 3.45 Å
AuthorsToth, E.A. / Li, Y. / Sawaya, M.R. / Cheng, Y. / Ellenberger, T.
CitationJournal: Mol.Cell / Year: 2003
Title: The Crystal Structure of the Bifunctional Primase-Helicase of Bacteriophage T7
Authors: Toth, E.A. / Li, Y. / Sawaya, M.R. / Cheng, Y. / Ellenberger, T.
History
DepositionAug 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 7 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 7 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE THAT THE HEPTAMER IS THE BIOLOGICAL UNIT, ALTHOUGH THE ENZYME IS NORMALLY A HEXAMER. THE AUTHORS DO NOT KNOW WHAT THE EXACT ROLE OF THE HEPTAMER IS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA primase/helicase
B: DNA primase/helicase
C: DNA primase/helicase
D: DNA primase/helicase
E: DNA primase/helicase
F: DNA primase/helicase
G: DNA primase/helicase


Theoretical massNumber of molelcules
Total (without water)390,9997
Polymers390,9997
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23190 Å2
ΔGint-94 kcal/mol
Surface area144060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.179, 171.567, 118.581
Angle α, β, γ (deg.)90.00, 99.86, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81A
91B
101C
111D
121E
131F
141G
12A
22B
32C
42D
52E
62F
72G
13A
23B
33C
43D
53E
63F
73G

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETTRPTRP1AA64 - 2551 - 192
211METMETTRPTRP1BB64 - 2551 - 192
311METMETTRPTRP1CC64 - 2551 - 192
411METMETTRPTRP1DD64 - 2551 - 192
511METMETTRPTRP1EE64 - 2551 - 192
611METMETTRPTRP1FF64 - 2551 - 192
711METMETTRPTRP1GG64 - 2551 - 192
821ASNASNILEILE4AA256 - 261193 - 198
921ASNASNILEILE4BB256 - 261193 - 198
1021ASNASNILEILE4CC256 - 261193 - 198
1121ASNASNILEILE4DD256 - 261193 - 198
1221ASNASNILEILE4EE256 - 261193 - 198
1321ASNASNILEILE4FF256 - 261193 - 198
1421ASNASNILEILE4GG256 - 261193 - 198
112PROPROGLUGLU1AA262 - 283199 - 220
212PROPROGLUGLU1BB262 - 283199 - 220
312PROPROGLUGLU1CC262 - 283199 - 220
412PROPROGLUGLU1DD262 - 283199 - 220
512PROPROGLUGLU1EE262 - 283199 - 220
612PROPROGLUGLU1FF262 - 283199 - 220
712PROPROGLUGLU1GG262 - 283199 - 220
113SERSERGLYGLY1AA284 - 549221 - 486
213SERSERGLYGLY1BB284 - 549221 - 486
313SERSERGLYGLY1CC284 - 549221 - 486
413SERSERGLYGLY1DD284 - 549221 - 486
513SERSERGLYGLY1EE284 - 549221 - 486
613SERSERGLYGLY1FF284 - 549221 - 486
713SERSERGLYGLY1GG284 - 549221 - 486

NCS ensembles :
ID
1
2
3
Detailsheptamer, a full heptamer is contained in the asymmetric unit

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Components

#1: Protein
DNA primase/helicase


Mass: 55856.965 Da / Num. of mol.: 7 / Mutation: G317V, K318M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: 4 / Production host: Escherichia coli (E. coli)
References: UniProt: P03692, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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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 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: MES, sodium citrate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 MMES1reservoirpH6.0
30.81-0.855 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2002
RadiationMonochromator: Si(111) or (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.45→116.8 Å / Num. all: 60625 / Num. obs: 60625 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.044 / Net I/σ(I): 29.1
Reflection shellResolution: 3.45→3.57 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.506 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.506

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Processing

Software
NameVersionClassification
REFMAC5.1.80refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD, MIR / Resolution: 3.45→20 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.884 / SU B: 40.915 / SU ML: 0.63 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.775 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.32597 3055 5.1 %RANDOM
Rwork0.29943 ---
all0.30077 57224 --
obs0.30077 57224 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 138.412 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å2-2.38 Å2
2--5.42 Å20 Å2
3----4.94 Å2
Refinement stepCycle: LAST / Resolution: 3.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26208 0 0 0 26208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02126648
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.9535874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.73153367
X-RAY DIFFRACTIONr_chiral_restr0.1140.23934
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219988
X-RAY DIFFRACTIONr_nbd_refined0.2760.211159
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4340.2126
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1502tight positional0.540.05
12B1502tight positional0.160.05
13C1502tight positional0.10.05
14D1502tight positional0.10.05
15E1502tight positional0.10.05
16F1502tight positional0.150.05
17G1502tight positional0.140.05
21A173tight positional0.090.05
22B173tight positional0.210.05
23C173tight positional0.080.05
24D173tight positional0.090.05
25E173tight positional0.110.05
26F173tight positional0.090.05
27G173tight positional0.290.05
31A2023tight positional0.120.05
32B2023tight positional0.10.05
33C2023tight positional0.210.05
34D2023tight positional0.080.05
35E2023tight positional0.120.05
36F2023tight positional0.10.05
37G2023tight positional0.080.05
11A46medium positional1.070.5
12B46medium positional1.110.5
13C46medium positional1.150.5
14D46medium positional1.230.5
15E46medium positional0.720.5
16F46medium positional0.750.5
17G46medium positional1.130.5
LS refinement shellResolution: 3.45→3.537 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.362 210
Rwork0.364 3988
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)
13.3669-0.2240.353611.35590.82724.77930.39920.43670.0286-0.2410.0777-0.09740.34490.2036-0.47690.78230.0956-0.13541.0088-0.33710.940990.016610.060827.5404
23.5837-4.89832.94985.3135-2.52765.03-0.1901-0.72260.4080.62510.64550.05580.35-0.3927-0.45540.6693-0.1140.01191.2177-0.12620.710560.907159.90770.534
34.4723-0.0503-1.60179.57590.29552.90140.08820.3928-0.24151.2943-0.51960.85580.4777-0.3160.43141.3259-0.19520.26521.206-0.38551.33251.76719.500851.5868
43.6963-0.2362-0.48695.8141-1.37186.4694-0.18990.86130.43460.07410.07830.593-0.2567-0.4730.11160.6230.0994-0.01761.0602-0.10930.896477.202454.554629.6673
53.4633-0.7378-0.853213.258-0.01775.28550.29420.2131-0.0505-0.2652-0.3484-0.63610.00750.30040.05420.94570.0732-0.24640.39610.33260.905669.943819.618-17.3915
67.0288-0.96990.36414.49560.54353.3145-0.0127-0.7546-0.27470.45920.35710.25370.6757-0.2147-0.34440.9386-0.0844-0.04890.71720.2420.527.368969.2044-4.0084
77.47083.33472.997910.67251.11228.54980.4477-0.0961-0.48070.9982-0.548-0.25580.4246-0.61730.10030.9778-0.23250.09210.2117-0.0880.28974.558139.1394-29.8798
86.272-0.3173-5.2083.00732.07357.2874-0.104-0.7593-0.0172-0.09280.3893-0.7646-0.35780.7316-0.28530.5576-0.2024-0.00650.84920.38130.86262.365370.066818.0725
91.95853.06353.396812.92989.85468.33830.5367-0.2762-0.5688-0.5695-0.1392-0.30950.2372-0.7493-0.39741.71280.02740.33871.6249-0.42521.4954-10.693631.5187-1.9553
101.98651.00422.2182.9193-0.54328.59080.25660.3486-0.35840.19830.049-0.9930.46090.2885-0.30560.7671-0.1514-0.22320.78660.15871.12684.044264.707553.0269
115.24451.64720.55659.69322.03077.27010.64940.1094-0.2290.9844-0.1014-0.94690.57620.3724-0.5480.84080.0193-0.25660.6998-0.23810.8879-13.59621.677752.3275
1210.65790.86134.57892.1187-0.60542.10080.28342.36770.323-1.28050.14920.46560.72891.5238-0.43260.86640.4345-0.07411.11440.01420.483231.790756.61871.4701
131.06021.7882-0.83224.70230.91240.5058-0.0237-0.2091-1.07380.7217-0.4789-0.36870.49920.02380.50261.7249-0.1093-0.35181.3768-0.1731.629113.283614.750375.0816
148.8073-0.3966-2.71753.5048-0.64974.0831-0.0120.07110.70570.26520.28140.7147-0.3652-0.8685-0.26940.8070.13390.24660.8573-0.19070.604164.45250.702460.5548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA64 - 2611 - 198
2X-RAY DIFFRACTION2AA262 - 549199 - 486
3X-RAY DIFFRACTION3BB64 - 2611 - 198
4X-RAY DIFFRACTION4BB262 - 549199 - 486
5X-RAY DIFFRACTION5CC64 - 2611 - 198
6X-RAY DIFFRACTION6CC262 - 549199 - 486
7X-RAY DIFFRACTION7DD64 - 2611 - 198
8X-RAY DIFFRACTION8DD262 - 549199 - 486
9X-RAY DIFFRACTION9EE64 - 2611 - 198
10X-RAY DIFFRACTION10EE262 - 549199 - 486
11X-RAY DIFFRACTION11FF64 - 2611 - 198
12X-RAY DIFFRACTION12FF262 - 549199 - 486
13X-RAY DIFFRACTION13GG64 - 2611 - 198
14X-RAY DIFFRACTION14GG262 - 549199 - 486
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.326 / Rfactor Rwork: 0.299
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.898

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