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- PDB-3u5z: Structure of T4 Bacteriophage clamp loader bound to the T4 clamp,... -

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Basic information

Entry
Database: PDB / ID: 3u5z
TitleStructure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog
Components
  • (DNA polymerase accessory protein ...) x 2
  • DNA polymerase processivity component
  • Primer DNA strand
  • Template DNA strand
KeywordsDNA BINDING PROTEIN/DNA / AAA+ / ATP hydrolase / clamp loader / sliding clamp / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA clamp loader activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA polymerase processivity factor activity / viral transcription / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Bacteriophage clamp loader A subunit, A domain / Bacteriophage clamp loader A subunit, A' domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1260 / Sliding-clamp-loader small subunit gp62 / Sliding-clamp-loader large subunit / : / : / Bacteriophage clamp loader A subunit / Sliding-clamp-loader large subunit, AAA+ ATPase lid domain / Sliding-clamp-loader large subunit, C-terminal domain ...Bacteriophage clamp loader A subunit, A domain / Bacteriophage clamp loader A subunit, A' domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1260 / Sliding-clamp-loader small subunit gp62 / Sliding-clamp-loader large subunit / : / : / Bacteriophage clamp loader A subunit / Sliding-clamp-loader large subunit, AAA+ ATPase lid domain / Sliding-clamp-loader large subunit, C-terminal domain / Sliding clamp, C-terminal / Sliding clamp / gp45 sliding clamp, C terminal / DNA polymerase processivity factor / DNA polymerase processivity factor / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Helicase, Ruva Protein; domain 3 - #60 / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helicase, Ruva Protein; domain 3 / Helix non-globular / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Special / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-08T / ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / Sliding clamp / Sliding-clamp-loader large subunit / Sliding-clamp-loader small subunit
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacementSAD / Resolution: 3.5 Å
AuthorsKelch, B.A. / Makino, D.L. / O'Donnell, M. / Kuriyan, J.
CitationJournal: Science / Year: 2011
Title: How a DNA polymerase clamp loader opens a sliding clamp.
Authors: Kelch, B.A. / Makino, D.L. / O'Donnell, M. / Kuriyan, J.
History
DepositionOct 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA polymerase accessory protein 44
C: DNA polymerase accessory protein 44
D: DNA polymerase accessory protein 44
E: DNA polymerase accessory protein 44
A: DNA polymerase accessory protein 62
G: DNA polymerase processivity component
H: DNA polymerase processivity component
F: DNA polymerase processivity component
I: Template DNA strand
J: Primer DNA strand
L: DNA polymerase accessory protein 44
M: DNA polymerase accessory protein 44
N: DNA polymerase accessory protein 44
O: DNA polymerase accessory protein 44
K: DNA polymerase accessory protein 62
Q: DNA polymerase processivity component
R: DNA polymerase processivity component
P: DNA polymerase processivity component
S: Template DNA strand
T: Primer DNA strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)520,99536
Polymers516,99320
Non-polymers4,00216
Water0
1
B: DNA polymerase accessory protein 44
C: DNA polymerase accessory protein 44
D: DNA polymerase accessory protein 44
E: DNA polymerase accessory protein 44
A: DNA polymerase accessory protein 62
G: DNA polymerase processivity component
H: DNA polymerase processivity component
F: DNA polymerase processivity component
I: Template DNA strand
J: Primer DNA strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,49718
Polymers258,49610
Non-polymers2,0018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33610 Å2
ΔGint-164 kcal/mol
Surface area93840 Å2
MethodPISA
2
L: DNA polymerase accessory protein 44
M: DNA polymerase accessory protein 44
N: DNA polymerase accessory protein 44
O: DNA polymerase accessory protein 44
K: DNA polymerase accessory protein 62
Q: DNA polymerase processivity component
R: DNA polymerase processivity component
P: DNA polymerase processivity component
S: Template DNA strand
T: Primer DNA strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,49718
Polymers258,49610
Non-polymers2,0018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33320 Å2
ΔGint-170 kcal/mol
Surface area94880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.702, 239.177, 247.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
32
42
52
62
13
23
14
24
34
44
15
25
16
26
17
27
37
47
18
28
19
29
39
49
59
69
79
89
110
210
111
211
112
212

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain D and resid 1:16
211chain N and resid 1:16
112chain A and resid 1:16
212chain B and resid 1:16
312chain C and resid 1:16
412chain K and resid 1:16
512chain L and resid 1:16
612chain M and resid 1:16
113chain A and resid 17:158
213chain K and resid 17:158
114chain B and resid 17:158
214chain C and resid 17:158
314chain L and resid 17:158
414chain M and resid 17:158
115chain D and resid 17:158
215chain N and resid 17:158
116chain A and resid 159:230
216chain K and resid 159:230
117chain B and resid 159:230
217chain C and resid 159:230
317chain L and resid 159:230
417chain M and resid 159:230
118chain D and resid 159:230
218chain N and resid 159:230
119chain A and resid 234:316
219chain B and resid 234:316
319chain C and resid 234:316
419chain D and resid 234:316
519chain K and resid 234:316
619chain L and resid 234:316
719chain M and resid 234:316
819chain N and resid 234:316
1110chain E and resid 1:34
2110chain O and resid 1:34
1111chain E and resid 36:111
2111chain O and resid 36:111
1112chain E and resid 112:199
2112chain O and resid 112:199

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

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DNA polymerase accessory protein ... , 2 types, 10 molecules BCDELMNOAK

#1: Protein
DNA polymerase accessory protein 44 / Clamp loader large subunit / Protein Gp44


Mass: 36189.602 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 44, gp44 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P04526
#2: Protein DNA polymerase accessory protein 62 / Clamp loader small subunit / Protein Gp62


Mass: 22941.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 62, gp62 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P04527

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Protein , 1 types, 6 molecules GHFQRP

#3: Protein
DNA polymerase processivity component / DNA polymerase accessory protein 45 / Gp45


Mass: 25162.592 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 45, gp45 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P04525

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DNA chain , 2 types, 4 molecules ISJT

#4: DNA chain Template DNA strand


Mass: 9172.891 Da / Num. of mol.: 2 / Source method: obtained synthetically
#5: DNA chain Primer DNA strand


Mass: 6136.008 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 3 types, 16 molecules

#6: Chemical
ChemComp-08T / [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium


Mass: 492.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14BeF3N5O10P2
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9% PEG4k, 0.1M MES pH 6.5, 50mM NaCl, 25mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 138392 / Num. obs: 137285 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rsym value: 0.16 / Net I/σ(I): 9.3
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.646 / % possible all: 90.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
AutoSolphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacementSAD / Resolution: 3.5→49.193 Å / SU ML: 1.08 / σ(F): 1.34 / Phase error: 28.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2787 1982 2.75 %Random
Rwork0.2309 ---
obs0.2322 72001 99.26 %-
all-72537 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.127 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--16.2438 Å20 Å2-0 Å2
2--14.4152 Å2-0 Å2
3---1.8286 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33376 1800 248 0 35424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01236231
X-RAY DIFFRACTIONf_angle_d1.67849352
X-RAY DIFFRACTIONf_dihedral_angle_d19.04613639
X-RAY DIFFRACTIONf_chiral_restr0.1075633
X-RAY DIFFRACTIONf_plane_restr0.0075976
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11D133X-RAY DIFFRACTIONPOSITIONAL
12N133X-RAY DIFFRACTIONPOSITIONAL0.05
21A141X-RAY DIFFRACTIONPOSITIONAL
22B141X-RAY DIFFRACTIONPOSITIONAL0.09
23C141X-RAY DIFFRACTIONPOSITIONAL0.093
24K141X-RAY DIFFRACTIONPOSITIONAL0.103
25L141X-RAY DIFFRACTIONPOSITIONAL0.067
26M141X-RAY DIFFRACTIONPOSITIONAL0.1
31A1084X-RAY DIFFRACTIONPOSITIONAL
32K1084X-RAY DIFFRACTIONPOSITIONAL0.047
41B1084X-RAY DIFFRACTIONPOSITIONAL
42C1084X-RAY DIFFRACTIONPOSITIONAL0.072
43L1084X-RAY DIFFRACTIONPOSITIONAL0.068
44M1084X-RAY DIFFRACTIONPOSITIONAL0.067
51D1084X-RAY DIFFRACTIONPOSITIONAL
52N1084X-RAY DIFFRACTIONPOSITIONAL0.053
61A560X-RAY DIFFRACTIONPOSITIONAL
62K560X-RAY DIFFRACTIONPOSITIONAL0.123
71B560X-RAY DIFFRACTIONPOSITIONAL
72C560X-RAY DIFFRACTIONPOSITIONAL0.083
73L560X-RAY DIFFRACTIONPOSITIONAL0.063
74M560X-RAY DIFFRACTIONPOSITIONAL0.082
81D491X-RAY DIFFRACTIONPOSITIONAL
82N491X-RAY DIFFRACTIONPOSITIONAL0.043
91A668X-RAY DIFFRACTIONPOSITIONAL
92B668X-RAY DIFFRACTIONPOSITIONAL0.083
93C668X-RAY DIFFRACTIONPOSITIONAL0.075
94D668X-RAY DIFFRACTIONPOSITIONAL0.072
95K668X-RAY DIFFRACTIONPOSITIONAL0.063
96L668X-RAY DIFFRACTIONPOSITIONAL0.065
97M668X-RAY DIFFRACTIONPOSITIONAL0.067
98N668X-RAY DIFFRACTIONPOSITIONAL0.067
101E273X-RAY DIFFRACTIONPOSITIONAL
102O273X-RAY DIFFRACTIONPOSITIONAL0.076
111E592X-RAY DIFFRACTIONPOSITIONAL
112O592X-RAY DIFFRACTIONPOSITIONAL0.051
121E614X-RAY DIFFRACTIONPOSITIONAL
122O614X-RAY DIFFRACTIONPOSITIONAL0.046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.5880.34771290.3074609X-RAY DIFFRACTION92
3.588-3.68490.3171470.2964939X-RAY DIFFRACTION99
3.6849-3.79330.27841350.27794932X-RAY DIFFRACTION100
3.7933-3.91570.38051400.27394931X-RAY DIFFRACTION100
3.9157-4.05560.31041420.25974992X-RAY DIFFRACTION100
4.0556-4.21790.29781400.24524972X-RAY DIFFRACTION100
4.2179-4.40980.27021380.22734999X-RAY DIFFRACTION100
4.4098-4.64210.2591400.20745002X-RAY DIFFRACTION100
4.6421-4.93270.26281470.20455005X-RAY DIFFRACTION100
4.9327-5.31310.3231420.235061X-RAY DIFFRACTION100
5.3131-5.8470.31671430.25465029X-RAY DIFFRACTION100
5.847-6.69130.32691470.23915076X-RAY DIFFRACTION100
6.6913-8.42350.25221440.19235134X-RAY DIFFRACTION100
8.4235-49.19790.18371480.1865338X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -36.0451 Å / Origin y: -18.6946 Å / Origin z: 25.2519 Å
111213212223313233
T0.7844 Å2-0.0806 Å20.047 Å2-0.7499 Å2-0.0452 Å2--0.6758 Å2
L0.7558 °2-0.251 °20.1586 °2-0.292 °2-0.1239 °2--0.2283 °2
S0.0081 Å °-0.0188 Å °-0.0325 Å °-0.0495 Å °0.0195 Å °-0.0083 Å °0.0277 Å °-0.0279 Å °0 Å °
Refinement TLS groupSelection details: all

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