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- PDB-5chi: Crystal structure of PF2046 in complex with ssDNA -

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Basic information

Entry
Database: PDB / ID: 5chi
TitleCrystal structure of PF2046 in complex with ssDNA
Components
  • DNA (5'-D(P*TP*TP*TP*T)-3')
  • Uncharacterized protein
KeywordsHYDROLASE/DNA / RnaseH / HYDROLASE-DNA complex
Function / homologyProtein of unknown function DUF4152 / Protein of unknown function DUF4152 / Protein of unknown function (DUF4152) / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / DNA / DUF4152 domain-containing protein
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.472 Å
Model detailscomplexed with dT4
AuthorsKim, J.S. / Hwang, K.Y. / Lee, W.C.
CitationJournal: to be published
Title: Structural basis of two-nucleotide removal of ssDNA by a cryptic RNase H fold 3'-5' exonuclease PF2046 from Pyrococcus furiosus
Authors: Kim, J.S. / Sambalkhundev, G.D. / Kim, S.H. / Han, A. / Ko, S.M. / Hwang, K.Y. / Lee, W.C.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: DNA (5'-D(P*TP*TP*TP*T)-3')
E: DNA (5'-D(P*TP*TP*TP*T)-3')
F: DNA (5'-D(P*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,89510
Polymers80,7986
Non-polymers974
Water1,856103
1
A: Uncharacterized protein
D: DNA (5'-D(P*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9814
Polymers26,9332
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-31 kcal/mol
Surface area10660 Å2
MethodPISA
2
B: Uncharacterized protein
E: DNA (5'-D(P*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9814
Polymers26,9332
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-30 kcal/mol
Surface area10640 Å2
MethodPISA
3
C: Uncharacterized protein
F: DNA (5'-D(P*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)26,9332
Polymers26,9332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-11 kcal/mol
Surface area10610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.010, 85.903, 69.204
Angle α, β, γ (deg.)90.000, 118.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 25760.812 Da / Num. of mol.: 3 / Fragment: PF2046
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF2046 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8TZE9
#2: DNA chain DNA (5'-D(P*TP*TP*TP*T)-3')


Mass: 1171.814 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Fragment: ion / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M sodium malonate, 0.1M Tris pH 8.0, 30% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 24745 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 6.57 % / Biso Wilson estimate: 41.92 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.145 / Χ2: 1.067 / Net I/σ(I): 12.54 / Num. measured all: 162455
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.47-2.620.7380.7092.119657410933190.77680.8
2.62-2.80.8880.5213.5127244385538450.56399.7
2.8-3.030.9520.3355.7324971361536010.36399.6
3.03-3.310.9750.2358.8322347333933290.25599.7
3.31-3.70.990.14314.2118822302130030.15799.4
3.7-4.270.9940.09620.8317226264826380.10499.6
4.27-5.230.9970.07126.9814742226022500.07799.6
5.23-7.370.9950.0725.3910923177317560.07699
7.370.9980.04636.746523101810040.0598.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPmodel building
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O8U

4o8u


Resolution: 2.472→34.588 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.88 / Phase error: 24.72 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2278 3832 7.94 %
Rwork0.1824 44413 -
obs0.186 24745 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.74 Å2 / Biso mean: 44.6629 Å2 / Biso min: 13.54 Å2
Refinement stepCycle: final / Resolution: 2.472→34.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5408 240 4 103 5755
Biso mean--41.35 37.51 -
Num. residues----699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015774
X-RAY DIFFRACTIONf_angle_d1.3587854
X-RAY DIFFRACTIONf_chiral_restr0.052888
X-RAY DIFFRACTIONf_plane_restr0.007961
X-RAY DIFFRACTIONf_dihedral_angle_d15.52212
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4717-2.5030.383180.599730031817
2.503-2.53590.38711560.31781537169390
2.5359-2.57060.30911330.266617141847100
2.5706-2.60730.34861510.261616881839100
2.6073-2.64620.31431360.257217151851100
2.6462-2.68760.34811140.247717161830100
2.6876-2.73160.28311680.255616521820100
2.7316-2.77870.29511500.238117301880100
2.7787-2.82920.26781410.225917211862100
2.8292-2.88360.28361160.218917311847100
2.8836-2.94240.29291650.225416901855100
2.9424-3.00640.27391250.220617221847100
3.0064-3.07620.32051670.213316931860100
3.0762-3.15310.23061360.216117201856100
3.1531-3.23830.28671580.214417031861100
3.2383-3.33350.25761480.197616851833100
3.3335-3.4410.24751640.187617081872100
3.441-3.56390.21511560.182616901846100
3.5639-3.70640.19831400.167717111851100
3.7064-3.87490.21991560.163216601816100
3.8749-4.07890.19861640.156617351899100
4.0789-4.3340.1871630.154316511814100
4.334-4.66790.20211380.141817211859100
4.6679-5.13630.17331480.135616871835100
5.1363-5.87640.21891390.163317181857100
5.8764-7.39170.17581450.157717111856100
7.3917-34.59110.13751370.136517041841100

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