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- PDB-2dla: Primase large subunit amino terminal domain from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 2dla
TitlePrimase large subunit amino terminal domain from Pyrococcus horikoshii
Components397aa long hypothetical protein
KeywordsREPLICATION / helix bundle / twisted beta-sheet
Function / homology
Function and homology information


DNA primase activity / primosome complex / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Transcription Elongation Factor S-II; Chain A - #50 / Phosphorylase Kinase; domain 1 - #260 / DNA primase large subunit PriL / DNA primase large subunit, eukaryotic/archaeal / Eukaryotic and archaeal DNA primase, large subunit / Transcription Elongation Factor S-II; Chain A / Phosphorylase Kinase; domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA primase large subunit PriL
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsIto, N.
CitationJournal: Febs J. / Year: 2007
Title: Molecular basis for the subunit assembly of the primase from an archaeon Pyrococcus horikoshii
Authors: Ito, N. / Matsui, I. / Matsui, E.
History
DepositionApr 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 397aa long hypothetical protein
B: 397aa long hypothetical protein
C: 397aa long hypothetical protein


Theoretical massNumber of molelcules
Total (without water)78,5053
Polymers78,5053
Non-polymers00
Water30617
1
A: 397aa long hypothetical protein


Theoretical massNumber of molelcules
Total (without water)26,1681
Polymers26,1681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 397aa long hypothetical protein


Theoretical massNumber of molelcules
Total (without water)26,1681
Polymers26,1681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 397aa long hypothetical protein


Theoretical massNumber of molelcules
Total (without water)26,1681
Polymers26,1681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: 397aa long hypothetical protein
B: 397aa long hypothetical protein


Theoretical massNumber of molelcules
Total (without water)52,3372
Polymers52,3372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-14 kcal/mol
Surface area21660 Å2
MethodPISA
5
C: 397aa long hypothetical protein

C: 397aa long hypothetical protein


Theoretical massNumber of molelcules
Total (without water)52,3372
Polymers52,3372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area1310 Å2
ΔGint-13 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.250, 89.250, 252.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 397aa long hypothetical protein / Primase large subunit


Mass: 26168.283 Da / Num. of mol.: 3 / Fragment: residues 1-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 3256582, UniProt: O57935*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M Ammonium Sulfate, 50mM Magnesium Sulfate, 25mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL41XU20.9793, 0.9795, 0.9840, 0.9717
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJul 7, 2003
MAR CCD 165 mm2CCDOct 21, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97931
30.97951
40.9841
50.97171
ReflectionResolution: 2.9→50 Å / Num. all: 23616 / Num. obs: 23431 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 56.447 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 17
Reflection shellResolution: 2.9→2.93 Å / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 7.3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
MLPHAREphasing
CNS1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT
Starting model: seleno-methionie derivative structure(This is not deposited to PDB)

Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3094 21250 RANDOM
Rwork0.2482 --
all-23360 -
obs-22869 -
Displacement parametersBiso mean: 26.3411 Å2
Baniso -1Baniso -2Baniso -3
1--5 Å20 Å20 Å2
2---5 Å20 Å2
3---10.001 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-20 Å
Luzzati sigma a0.57 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5272 0 0 17 5289
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00829
X-RAY DIFFRACTIONc_angle_deg1.36362
X-RAY DIFFRACTIONc_dihedral_angle_d20.49354
X-RAY DIFFRACTIONc_improper_angle_d0.79216

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