- PDB-4bpw: Crystal structure of human primase bound to UTP -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4bpw
Title
Crystal structure of human primase bound to UTP
Components
DNA PRIMASE LARGE SUBUNIT
DNA PRIMASE SMALL SUBUNIT
Keywords
TRANSFERASE / DNA-DEPENDENT RNA POLYMERASE / DNA REPLICATION
Function / homology
Function and homology information
positive regulation of DNA primase activity / DNA primase AEP / ribonucleotide binding / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand ...positive regulation of DNA primase activity / DNA primase AEP / ribonucleotide binding / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / DNA primase activity / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / DNA replication, synthesis of primer / Activation of the pre-replicative complex / DNA replication initiation / Defective pyroptosis / 4 iron, 4 sulfur cluster binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm / membrane / metal ion binding Similarity search - Function
Transcription Elongation Factor S-II; Chain A - #80 / DNA primase, PRIM domain / DNA primase, PRIM domain / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, large subunit, eukaryotic / DNA primase, small subunit / DNA primase small subunit / DNA primase large subunit, eukaryotic/archaeal / Eukaryotic and archaeal DNA primase, large subunit / Transcription Elongation Factor S-II; Chain A ...Transcription Elongation Factor S-II; Chain A - #80 / DNA primase, PRIM domain / DNA primase, PRIM domain / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, large subunit, eukaryotic / DNA primase, small subunit / DNA primase small subunit / DNA primase large subunit, eukaryotic/archaeal / Eukaryotic and archaeal DNA primase, large subunit / Transcription Elongation Factor S-II; Chain A / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal grow
Details: 100MM TRIS-HCL/BICINE PH 8.5, 20% GLYCEROL, 10% PEG4000 AND 20MM EACH OF AN ALCOHOL MIX COMPRISING 1,6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4-BUTANEDIOL AND 1,3-PROPANEDIOL.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9795 Å / Relative weight: 1
Reflection
Resolution: 3→48.87 Å / Num. obs: 39304 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 105.46 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.5
Reflection shell
Resolution: 3→3.13 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.2 / % possible all: 98.6
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
Aimless
datascaling
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 3.003→46.784 Å / SU ML: 0.5 / σ(F): 1.27 / Phase error: 32.12 / Stereochemistry target values: ML Details: THE STRUCTURE WAS REFINED IN PHENIX WITH RIDING HYDROGENS. THE HYDROGENS HAVE BEEN INCLUDED IN THE ENTRY.
Rfactor
Num. reflection
% reflection
Rfree
0.2534
3832
5.1 %
Rwork
0.2152
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obs
0.2172
39252
98.28 %
Solvent computation
Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 94.6 Å2
Refinement step
Cycle: LAST / Resolution: 3.003→46.784 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9784
0
64
0
9848
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
10087
X-RAY DIFFRACTION
f_angle_d
0.924
13608
X-RAY DIFFRACTION
f_dihedral_angle_d
12.629
3848
X-RAY DIFFRACTION
f_chiral_restr
0.037
1460
X-RAY DIFFRACTION
f_plane_restr
0.004
1719
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.0026-3.0406
0.4662
125
0.4547
2468
X-RAY DIFFRACTION
92
3.0406-3.0806
0.4371
113
0.4293
2731
X-RAY DIFFRACTION
98
3.0806-3.1228
0.4276
146
0.383
2618
X-RAY DIFFRACTION
99
3.1228-3.1674
0.4157
155
0.3663
2692
X-RAY DIFFRACTION
99
3.1674-3.2147
0.433
126
0.3492
2668
X-RAY DIFFRACTION
99
3.2147-3.2649
0.3775
119
0.3325
2662
X-RAY DIFFRACTION
99
3.2649-3.3184
0.3872
157
0.3208
2689
X-RAY DIFFRACTION
99
3.3184-3.3756
0.3572
149
0.2996
2638
X-RAY DIFFRACTION
99
3.3756-3.437
0.3368
140
0.2907
2671
X-RAY DIFFRACTION
99
3.437-3.5031
0.3204
130
0.2821
2683
X-RAY DIFFRACTION
99
3.5031-3.5746
0.3
131
0.2574
2657
X-RAY DIFFRACTION
99
3.5746-3.6522
0.2869
140
0.2457
2747
X-RAY DIFFRACTION
99
3.6522-3.7372
0.2709
151
0.2249
2637
X-RAY DIFFRACTION
99
3.7372-3.8306
0.2745
164
0.2253
2652
X-RAY DIFFRACTION
99
3.8306-3.9341
0.255
173
0.2183
2622
X-RAY DIFFRACTION
99
3.9341-4.0498
0.2844
145
0.2153
2679
X-RAY DIFFRACTION
99
4.0498-4.1805
0.2352
141
0.1989
2697
X-RAY DIFFRACTION
99
4.1805-4.3298
0.235
157
0.1927
2689
X-RAY DIFFRACTION
99
4.3298-4.503
0.2265
139
0.1794
2685
X-RAY DIFFRACTION
99
4.503-4.7077
0.2116
110
0.1769
2695
X-RAY DIFFRACTION
99
4.7077-4.9557
0.2317
138
0.1803
2683
X-RAY DIFFRACTION
99
4.9557-5.2658
0.2386
146
0.1885
2651
X-RAY DIFFRACTION
99
5.2658-5.6717
0.2489
151
0.1982
2682
X-RAY DIFFRACTION
99
5.6717-6.2413
0.2514
163
0.2121
2641
X-RAY DIFFRACTION
98
6.2413-7.1417
0.2511
128
0.2139
2638
X-RAY DIFFRACTION
98
7.1417-8.9873
0.1901
146
0.1863
2614
X-RAY DIFFRACTION
97
8.9873-46.7895
0.22
149
0.1804
2439
X-RAY DIFFRACTION
91
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