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- PDB-1nui: Crystal Structure of the primase fragment of Bacteriophage T7 pri... -

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Basic information

Entry
Database: PDB / ID: 1nui
TitleCrystal Structure of the primase fragment of Bacteriophage T7 primase-helicase protein
ComponentsDNA primase/helicase
KeywordsREPLICATION / zinc-biding domain / TOPRIM fold / DNA replication / DNA-directed RNA polymerase / Primosome / Late protein / ATP-binding / Transferase
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
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 / Twinkle-like protein / Archaeal primase DnaG/twinkle-like, TOPRIM domain / Toprim-like / DnaB-like helicase C terminal domain ...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 / 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 - #10 / N-terminal domain of TfIIb / Toprim domain profile. / TOPRIM domain / Single Sheet / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
DNA helicase/primase
Similarity search - Component
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsKato, M. / Ito, T. / Wagner, G. / Richardson, C.C. / Ellenberger, T.
CitationJournal: Mol.Cell / Year: 2003
Title: Modular Architecture of the Bacteriophage T7 Primase Couples RNA primer Synthesis to DNA Synthesis
Authors: Kato, M. / Ito, T. / Wagner, G. / Richardson, C.C. / Ellenberger, T.
History
DepositionJan 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 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 / 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 1.4Feb 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 300biomelecule:1, 2 The author indicates that the protein can function as a monomer but appears to ...biomelecule:1, 2 The author indicates that the protein can function as a monomer but appears to form a dimer in the crystal possibly due to crystal packing forces. See remark 350 for information on generating the biological molecule(s).

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0308
Polymers56,8022
Non-polymers2286
Water25214
1
A: DNA primase/helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5154
Polymers28,4011
Non-polymers1143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA primase/helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5154
Polymers28,4011
Non-polymers1143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.459, 136.460, 85.445
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLUGLU6AA10 - 4010 - 40
21VALVALGLUGLU6BB10 - 4010 - 40
32LYSLYSTRPTRP5AA57 - 25557 - 255
42LYSLYSTRPTRP5BB57 - 25557 - 255

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Components

#1: Protein DNA primase/helicase


Mass: 28400.811 Da / Num. of mol.: 2 / Fragment: residues 1-255 / Mutation: M64G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: 4 / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P03692, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 4.34 Å3/Da / Density % sol: 71.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: Sodium Formate, MES, DTT, ATP, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
250 mMMES1droppH6.3
32 Msodium formate1drop
45.5 mMdithiothreitol1drop
52.5 mMATP1drop
6100 mMMES1reservoirpH6.3
74 Msodium formate1reservoir
85.5 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9474, 0.9797, 0.9795, 0.9300, 1.5418
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2002
RadiationMonochromator: Horizontal focussing 5.05 degree asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.94741
20.97971
30.97951
40.931
51.54181
ReflectionResolution: 2.6→65 Å / Num. all: 28599 / Num. obs: 28599 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.7
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.241 / % possible all: 93.6
Reflection
*PLUS
Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 93.6 %

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→10 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.859 / SU B: 15.135 / SU ML: 0.284 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.68 / ESU R Free: 0.364
RfactorNum. reflection% reflectionSelection details
Rfree0.27674 1029 5.1 %RANDOM
Rwork0.23452 ---
obs0.23665 19053 99.82 %-
all-19053 --
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: 19.593 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å21.05 Å20 Å2
2--2.1 Å20 Å2
3----3.14 Å2
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3763 0 6 14 3783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213843
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9295173
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.1735477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022940
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2930.22014
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2153
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3680.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0371.52371
X-RAY DIFFRACTIONr_mcangle_it2.02523779
X-RAY DIFFRACTIONr_scbond_it3.19131472
X-RAY DIFFRACTIONr_scangle_it5.3244.51394
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1551medium positional0.440.5
238loose positional5.375
1551medium thermal1.572
238loose thermal310
LS refinement shellResolution: 2.9→2.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 65 -
Rwork0.325 1303 -
obs-1368 99.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
114.9892-12.0978-8.251811.740810.193819.8698-0.8520.0913-0.89331.2635-0.29760.24121.03750.9241.14960.5033-0.1964-0.08430.53220.08010.487490.172549.097321.9643
29.64410.66443.43061.905-0.36484.3323-0.34470.77080.9336-0.19350.1510.134-0.37360.26070.19370.1451-0.039-0.08570.53870.14440.338949.704769.854219.5145
326.401614.9794-11.594811.5727-15.311611.8456-1.17750.3064-0.4971-0.28420.42540.2149-0.4126-0.2590.75210.56780.0876-0.06570.6547-0.14570.440642.384353.753139.8301
44.57070.14491.32571.4009-0.03594.1364-0.07120.1234-0.0803-0.14110.06680.1447-0.0217-0.28240.00440.0368-0.0778-0.02690.2587-0.06010.165182.5764.715741.4902
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 4410 - 44
2X-RAY DIFFRACTION2AA49 - 25549 - 255
3X-RAY DIFFRACTION3BB10 - 4210 - 42
4X-RAY DIFFRACTION4BB50 - 25550 - 255
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.46
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg1.18

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