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- PDB-3p83: Structure of the PCNA:RNase HII complex from Archaeoglobus fulgidus. -

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Basic information

Entry
Database: PDB / ID: 3p83
TitleStructure of the PCNA:RNase HII complex from Archaeoglobus fulgidus.
Components
  • DNA polymerase sliding clamp
  • Ribonuclease HII
KeywordsHYDROLASE/DNA BINDING PROTEIN / DNA clamp / RNase H fold / cleaves RNA/DNA hybrids / nucleus / HYDROLASE-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


ribonuclease H2 complex / DNA replication, removal of RNA primer / ribonuclease H / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / RNA-DNA hybrid ribonuclease activity / manganese ion binding / DNA binding ...ribonuclease H2 complex / DNA replication, removal of RNA primer / ribonuclease H / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / RNA-DNA hybrid ribonuclease activity / manganese ion binding / DNA binding / RNA binding / cytoplasm
Similarity search - Function
Ribonuclease HII, archaea / Ribonuclease hii. Domain 2 / Ribonuclease HII, helix-loop-helix cap domain superfamily / Ribonuclease H2, subunit A / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / Ribonuclease (RNase) H type-2 domain profile. / Box / Proliferating Cell Nuclear Antigen ...Ribonuclease HII, archaea / Ribonuclease hii. Domain 2 / Ribonuclease HII, helix-loop-helix cap domain superfamily / Ribonuclease H2, subunit A / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / Ribonuclease (RNase) H type-2 domain profile. / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / : / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribonuclease HII / DNA polymerase sliding clamp
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsBubeck, D. / Reijns, M.A. / Graham, S.C. / Astell, K.R. / Jones, E.Y. / Jackson, A.P.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: PCNA directs type 2 RNase H activity on DNA replication and repair substrates.
Authors: Bubeck, D. / Reijns, M.A. / Graham, S.C. / Astell, K.R. / Jones, E.Y. / Jackson, A.P.
History
DepositionOct 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 8, 2014Group: Structure summary
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase sliding clamp
B: DNA polymerase sliding clamp
C: DNA polymerase sliding clamp
D: Ribonuclease HII
E: Ribonuclease HII
F: Ribonuclease HII


Theoretical massNumber of molelcules
Total (without water)155,1986
Polymers155,1986
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-29 kcal/mol
Surface area56930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.670, 152.030, 90.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA polymerase sliding clamp / Proliferating cell nuclear antigen homolog / PCNA


Mass: 27301.521 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: pcn, AF_0335 / Plasmid: Gift from J. Tainer / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 / References: UniProt: O29912
#2: Protein Ribonuclease HII / RNase HII


Mass: 24431.246 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_0621, rnhB / Plasmid: based on pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 / References: UniProt: O29634, ribonuclease H
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: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9.2
Details: 18% PEG 3350, 196mM K2HPO4, pH 9.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.01→44.54 Å / Num. all: 39748 / Num. obs: 39748 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 89.01 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 15.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.9.2refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RXM and PDB ENTRY 1I39

1rxm

1i39


Resolution: 3.05→44.54 Å / Cor.coef. Fo:Fc: 0.9299 / Cor.coef. Fo:Fc free: 0.9081 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 1996 5.02 %RANDOM
Rwork0.1868 ---
all0.1882 39739 --
obs0.1882 39739 --
Displacement parametersBiso mean: 77.46 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2---11.8081 Å20 Å2
3---10.6281 Å2
Refine analyzeLuzzati coordinate error obs: 0.576 Å
Refinement stepCycle: LAST / Resolution: 3.05→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10465 0 0 0 10465
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.009106082
X-RAY DIFFRACTIONt_angle_deg1.08142962
X-RAY DIFFRACTIONt_dihedral_angle_d38812
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes2612
X-RAY DIFFRACTIONt_gen_planes15265
X-RAY DIFFRACTIONt_it1060820
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion18.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion14395
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact122974
LS refinement shellResolution: 3.05→3.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3042 127 4.62 %
Rwork0.2575 2622 -
all0.2596 2749 -
obs-2749 -
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)
12.7510.5538-0.10781.32580.17191.6469-0.0211-0.1437-0.15820.2561-0.02950.0640.14410.01030.05050.0750.09570.0553-0.21440.0384-0.076732.511523.644721.0564
22.7546-0.4849-0.29743.14291.29062.587-0.1891-0.3150.16610.37530.16040.0035-0.03840.02760.0287-0.11130.07650.1094-0.03990.0669-0.2278-1.346546.011138.8506
34.2448-1.5639-1.3542.75691.66572.1786-0.0151-0.46450.53330.3051-0.06260.0513-0.0222-0.12710.07760.059-0.0572-0.152-0.1602-0.142-0.201540.276962.452640.2247
40.3152-0.5168-0.04654.5367-0.91421.04290.1082-0.00310.051-0.3406-0.0970.0314-0.09440.1882-0.0112-0.0585-0.01710.0147-0.10870.00460.059943.305260.5237-8.2667
500.1061-2.244700.57370.1006-0.00820.1183-0.0585-0.04130.04820.11380.03930.0431-0.03990.20660.02480.1276-0.2049-0.06370.008741.139824.53484.4877
63.83861.1581-1.67983.5575-1.15553.06930.0938-0.22440.31990.2825-0.01620.2686-0.2097-0.2283-0.0775-0.1365-0.02970.0452-0.1379-0.0078-0.136918.963461.763415.3972
70-0.46260.26650.3881-0.032700.0062-0.00120.0444-0.012-0.00310.0042-0.02680.0158-0.00310.07420.0882-0.0405-0.1465-0.15190.051738.856780.278435.0151
83.13582.5284-2.67093.7381-2.91047.9546-0.29710.5442-0.0552-0.53790.1952-0.31420.16570.54420.1019-0.2488-0.1520.04910.0694-0.0896-0.28762.207148.3707-7.5687
90.1234-0.13840.814400.80620.00030.01050.01210.0389-0.0332-0.01780.1014-0.03850.00140.0074-0.2180.1214-0.06240.17720.0244-0.0442-14.127346.022924.9254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 244
2X-RAY DIFFRACTION2{ B|* }B1 - 244
3X-RAY DIFFRACTION3{ C|* }C1 - 243
4X-RAY DIFFRACTION4tlsDsetD-7 - 199
5X-RAY DIFFRACTION5{ D|200 - D|205 }D200 - 205
6X-RAY DIFFRACTION6tlsEsetE0 - 199
7X-RAY DIFFRACTION7{ E|200 - E|205 }E200 - 205
8X-RAY DIFFRACTION8tlsFsetF1 - 199
9X-RAY DIFFRACTION9{ F|200 - F|205 }F200 - 205

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