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- PDB-8jrb: Structure of DNA polymerase 1 from Aquifex pyrophilus -

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Basic information

Entry
Database: PDB / ID: 8jrb
TitleStructure of DNA polymerase 1 from Aquifex pyrophilus
ComponentsDNA polymerase I
KeywordsREPLICATION / DNA Polymerase
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / Ribonuclease H superfamily ...3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesAquifex pyrophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsClement, P. / Nair, D.T.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)C09001 India
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: A conserved polar residue plays a critical role in mismatch detection in A-family DNA polymerases.
Authors: Clement, P.C. / Sapam, T. / Nair, D.T.
History
DepositionJun 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase I
B: DNA polymerase I


Theoretical massNumber of molelcules
Total (without water)137,2512
Polymers137,2512
Non-polymers00
Water7,404411
1
A: DNA polymerase I


Theoretical massNumber of molelcules
Total (without water)68,6251
Polymers68,6251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase I


Theoretical massNumber of molelcules
Total (without water)68,6251
Polymers68,6251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.826, 74.725, 129.560
Angle α, β, γ (deg.)90.000, 108.250, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 263 or resid 265 through 574))
d_2ens_1(chain "B" and (resid 1 through 263 or resid 265 through 574))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETGLYGLYAA1 - 26324 - 286
d_12VALVALASPASPAA265 - 574288 - 597
d_21METMETGLYGLYBB1 - 26324 - 286
d_22VALVALASPASPBB265 - 574288 - 597

NCS oper: (Code: givenMatrix: (-0.762028618176, -0.564237857745, -0.31772318922), (-0.570800090603, 0.353607030974, 0.741046101274), (-0.305777111062, 0.746054761752, -0.591525697513)Vector: -38. ...NCS oper: (Code: given
Matrix: (-0.762028618176, -0.564237857745, -0.31772318922), (-0.570800090603, 0.353607030974, 0.741046101274), (-0.305777111062, 0.746054761752, -0.591525697513)
Vector: -38.3831801117, -28.9417163154, 23.9742209246)

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Components

#1: Protein DNA polymerase I


Mass: 68625.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex pyrophilus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: Q8GHE9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 3 Å3/Da / Density % sol: 58.96 % / Description: Flat Plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 18% PEG 8K, 100 mM Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.2→48.91 Å / Num. obs: 80316 / % possible obs: 97.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 44.38 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.031 / Net I/σ(I): 15.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.9 % / Num. unique obs: 4294 / CC1/2: 0.669 / Rpim(I) all: 0.505 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.26 Å / SU ML: 0.2983 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 25.6713
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2329 7766 5.1 %
Rwork0.1909 144633 -
obs0.193 80236 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9287 0 0 411 9698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079441
X-RAY DIFFRACTIONf_angle_d1.261412692
X-RAY DIFFRACTIONf_chiral_restr0.06141434
X-RAY DIFFRACTIONf_plane_restr0.00751611
X-RAY DIFFRACTIONf_dihedral_angle_d8.35451256
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.98673379328 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.36192510.30624789X-RAY DIFFRACTION96.59
2.23-2.250.44552350.37524091X-RAY DIFFRACTION79.06
2.25-2.280.34992740.30454776X-RAY DIFFRACTION94.85
2.28-2.310.31993030.2644980X-RAY DIFFRACTION96.62
2.31-2.340.27772670.24554852X-RAY DIFFRACTION96.13
2.34-2.370.28822470.23285001X-RAY DIFFRACTION96.72
2.37-2.40.28162460.23224983X-RAY DIFFRACTION96.62
2.4-2.440.282540.23064914X-RAY DIFFRACTION96.72
2.44-2.480.23332410.22444990X-RAY DIFFRACTION96.74
2.48-2.520.2792600.22354892X-RAY DIFFRACTION96.68
2.52-2.560.28452470.23315002X-RAY DIFFRACTION96.67
2.56-2.610.24672530.22944915X-RAY DIFFRACTION96.53
2.61-2.660.36042970.23594789X-RAY DIFFRACTION94.17
2.66-2.710.33572460.24524475X-RAY DIFFRACTION87.41
2.71-2.770.23722650.22534985X-RAY DIFFRACTION96.7
2.77-2.840.26962790.21794830X-RAY DIFFRACTION96.09
2.84-2.910.2912390.21875014X-RAY DIFFRACTION96.63
2.91-2.990.28882730.20084901X-RAY DIFFRACTION95.73
2.99-3.070.24022700.19824847X-RAY DIFFRACTION95.47
3.07-3.170.24873090.20934880X-RAY DIFFRACTION96.97
3.17-3.290.25532580.19784952X-RAY DIFFRACTION96.2
3.29-3.420.21612670.19224891X-RAY DIFFRACTION95.43
3.42-3.570.21852460.19114582X-RAY DIFFRACTION89.41
3.57-3.760.23052410.1844728X-RAY DIFFRACTION92.26
3.76-40.2352320.17384550X-RAY DIFFRACTION88.95
4-4.310.16852710.14914768X-RAY DIFFRACTION93.35
4.31-4.740.17352230.14374798X-RAY DIFFRACTION93.43
4.74-5.420.22112510.16214827X-RAY DIFFRACTION93.24
5.42-6.830.20992920.19124834X-RAY DIFFRACTION95.3
6.83-46.260.17412290.15384797X-RAY DIFFRACTION93.47
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.026581712130.396024249155-0.8970205790051.90647222713-0.2504795406892.82862605003-0.01054204992550.137155867338-0.3759808413780.0504868451281-0.0245927846327-0.3750689688690.2783887777740.2855460764040.02225923882140.3921506019810.032967049507-0.05424142644180.365193130668-0.03325444187990.438726329086-20.066294492.7848378101540.1735969167
22.439345945320.0751991300448-0.8878651908810.300835830784-0.07442053886391.004741460950.113911788273-0.1239743940080.02777970359150.140355111259-0.0453949132739-0.0313324925809-0.2086219177220.110097473312-0.07214680666280.417555098746-0.000873914064007-0.03192499458450.300873823551-0.01108997320970.334428249119-30.946442044811.590207650148.0263977686
32.84253712194-0.5551385243861.074194995030.2563045189980.02160326134690.657961752984-0.02551940603780.4178806541950.23278102730.0660168111-0.102534098298-0.00372915060102-0.1795481673820.06961268926140.09146963724580.47493158915-0.02196791488750.06344206331020.435083593815-0.002220354351120.40398912382-66.782753773215.040664478231.6474390312
42.25673584878-0.0885218418999-0.2037180402361.093745457430.167316676360.644914245695-0.0400150314897-0.148666523043-0.2416670966340.0978010343141-0.01945013482670.0008135012378170.0481378295153-0.005145739652610.06237073381290.421904600211-0.01691272829650.01115919490480.2315807213680.02306586160690.266182697104-59.86364539833.6758811840956.3711243376
51.570651339011.22601149705-0.5140239804451.90767172556-0.3138620703170.912057461495-0.08494946065020.3960639454470.52529479989-0.1895572820160.1942282854130.6862981477960.0688265159739-0.341755622873-0.0945620005010.3044070801870.00770764281782-0.06712532604580.599386976650.03402232243530.530066164424-36.881060078721.68759496911.2850432375
61.441564235031.296505516541.194996638891.550300304860.4845515466581.90882959902-0.0396141118675-0.04435972666130.2187678717740.116526506105-0.1168329531450.306490250193-0.112521833638-0.3858304571720.1205266476480.3830807667660.01761698573780.002996398185560.41062975164-0.02931613409120.375427855405-2.771342470640.627808659541.7158189873
70.9512914755060.7177044408590.1457266648691.61597751847-0.05756245690240.570740096149-0.04316008635930.1157739816870.446211026646-0.001789244358420.07119266678940.385782067385-0.129600631921-0.123511651711-0.01643726939510.3658195508680.07555153685970.01686230117030.4794838682290.04345029313060.508949417945-13.241597618946.265270763112.8447381999
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 90 )AA1 - 901 - 90
22chain 'A' and (resid 91 through 209 )AA91 - 20991 - 209
33chain 'A' and (resid 210 through 334 )AA210 - 334210 - 334
44chain 'A' and (resid 335 through 574 )AA335 - 574335 - 574
55chain 'B' and (resid 1 through 209 )BB1 - 2091 - 209
66chain 'B' and (resid 210 through 303 )BB210 - 303210 - 303
77chain 'B' and (resid 304 through 574 )BB304 - 574304 - 574

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