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- PDB-1eqn: E.COLI PRIMASE CATALYTIC CORE -

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Basic information

Entry
Database: PDB / ID: 1eqn
TitleE.COLI PRIMASE CATALYTIC CORE
ComponentsDNA PRIMASE
KeywordsTRANSFERASE / Toprim domain / Rossmann fold
Function / homology
Function and homology information


DnaB-DnaG complex / DNA primase DnaG / primosome complex / DNA replication, synthesis of primer / replisome / replication fork processing / DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
DnaG, RNA polymerase domain, helical bundle / DNA primase, catalytic core, N-terminal domain / DNA primase DNAg catalytic core, N-terminal domain / DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / Pheromone ER-1 / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 ...DnaG, RNA polymerase domain, helical bundle / DNA primase, catalytic core, N-terminal domain / DNA primase DNAg catalytic core, N-terminal domain / DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / Pheromone ER-1 / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain / DNA primase, catalytic core, N-terminal domain superfamily / : / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / DNA Primase, CHC2-type zinc finger / Toprim-like / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / TOPRIM / Toprim domain profile. / TOPRIM domain / Alpha-Beta Complex / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsPodobnik, M. / McInerney, P. / O'Donnell, M. / Kuriyan, J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases.
Authors: Podobnik, M. / McInerney, P. / O'Donnell, M. / Kuriyan, J.
History
DepositionApr 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA PRIMASE
B: DNA PRIMASE
C: DNA PRIMASE
D: DNA PRIMASE
E: DNA PRIMASE


Theoretical massNumber of molelcules
Total (without water)183,1055
Polymers183,1055
Non-polymers00
Water00
1
A: DNA PRIMASE


Theoretical massNumber of molelcules
Total (without water)36,6211
Polymers36,6211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA PRIMASE


Theoretical massNumber of molelcules
Total (without water)36,6211
Polymers36,6211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA PRIMASE


Theoretical massNumber of molelcules
Total (without water)36,6211
Polymers36,6211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA PRIMASE


Theoretical massNumber of molelcules
Total (without water)36,6211
Polymers36,6211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: DNA PRIMASE


Theoretical massNumber of molelcules
Total (without water)36,6211
Polymers36,6211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.674, 107.626, 263.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer constructed from either chain A, B, C, D or E.

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Components

#1: Protein
DNA PRIMASE


Mass: 36620.941 Da / Num. of mol.: 5 / Fragment: CATALYTIC CORE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PPROEX-HTA / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABS5, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.21 %
Description: For the refinement the data from lambda 1 (0.98636) were taken.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 20 ℃
Details: drop consists of equal volume of protein and reservoir solutions
PH range low: 8.5 / PH range high: 7.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
216-19 %PEG40001reservoir
30.053-0.063 mMTris-HCl1reservoir
40.11-0.13 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.98636, 0.97939, 0.97900, 0.96526
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.986361
20.979391
30.9791
40.965261
ReflectionResolution: 2.9→20 Å / Num. all: 273234 / Num. obs: 272858 / % possible obs: 97.6 % / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 73.637 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 31.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.207 / Num. unique all: 13126 / % possible all: 90.8
Reflection
*PLUS
Num. obs: 40874 / Num. measured all: 273234
Reflection shell
*PLUS
% possible obs: 90.8 %

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.9→500 Å / σ(F): 2
Stereochemistry target values: Engh & Huber, Hendrickson W.A. and Konnert J.H.
Details: used standard crystallographic residual
RfactorNum. reflection% reflectionSelection details
Rfree0.276 6749 -RANDOM
Rwork0.2197 ---
all0.2393 75010 --
obs0.2259 67706 90.3 %-
Refinement stepCycle: LAST / Resolution: 2.9→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12156 0 0 0 12156
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0114
X-RAY DIFFRACTIONc_angle_d1.414

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