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- PDB-4pso: Crystal structure of apeThermo-DBP-RP2 bound to ssDNA dT10 -

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Basic information

Entry
Database: PDB / ID: 4pso
TitleCrystal structure of apeThermo-DBP-RP2 bound to ssDNA dT10
Components
  • polydeoxyribonucleotide
  • ssDNA binding protein
KeywordsDNA BINDING PROTEIN / ssDNA binding protein
Function / homology: / Thermo-DBP-RP2 C-terminal domain / ThermoDBP-related, archaea / ThermoDBP-related, archaea / PHOSPHATE ION / DNA / Thermo-DBP-RP2-like C-terminal domain-containing protein
Function and homology information
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGahlei, H. / von Moeller, H. / Eppers, D. / Loll, B. / Wahl, M.C.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein.
Authors: Ghalei, H. / Moeller, H.v. / Eppers, D. / Sohmen, D. / Wilson, D.N. / Loll, B. / Wahl, M.C.
History
DepositionMar 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ssDNA binding protein
B: ssDNA binding protein
C: ssDNA binding protein
D: ssDNA binding protein
F: ssDNA binding protein
G: ssDNA binding protein
H: ssDNA binding protein
I: ssDNA binding protein
L: polydeoxyribonucleotide
E: polydeoxyribonucleotide
X: polydeoxyribonucleotide
Z: polydeoxyribonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,10213
Polymers225,00712
Non-polymers951
Water68538
1
A: ssDNA binding protein
B: ssDNA binding protein
C: ssDNA binding protein
D: ssDNA binding protein
L: polydeoxyribonucleotide
E: polydeoxyribonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5997
Polymers112,5046
Non-polymers951
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23380 Å2
ΔGint-109 kcal/mol
Surface area38600 Å2
MethodPISA
2
F: ssDNA binding protein
G: ssDNA binding protein
H: ssDNA binding protein
I: ssDNA binding protein
X: polydeoxyribonucleotide
Z: polydeoxyribonucleotide


Theoretical massNumber of molelcules
Total (without water)112,5046
Polymers112,5046
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19960 Å2
ΔGint-77 kcal/mol
Surface area39960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.488, 190.277, 89.786
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-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain F
61chain G
71chain H
81chain I
12chain X
22chain Z

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVALchain AAA0 - 2173 - 220
21ALAALALYSLYSchain BBB-1 - 2182 - 221
31ALAALALYSLYSchain CCC-1 - 2182 - 221
41ALAALAVALVALchain DDD-1 - 2172 - 220
51METMETLYSLYSchain FFE0 - 2183 - 221
61METMETVALVALchain GGF0 - 2173 - 220
71ALAALALYSLYSchain HHG-1 - 2182 - 221
81GLYGLYLYSLYSchain IIH-2 - 2181 - 221
12DTDTDTDTchain XXK7 - 101 - 4
22DTDTDTDTchain ZZL11 - 141 - 4

NCS ensembles :
ID
1
2

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Components

#1: Protein
ssDNA binding protein


Mass: 26627.416 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea)
Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
Gene: APE_1866.1 / Plasmid: pET-M11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9YAS7
#2: DNA chain
polydeoxyribonucleotide


Mass: 2996.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: ssDNA oligonucleotide
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 200 mM NaOAc, pH 4.3, 1.3 M NaH2PO4 and 0.7 M K2HPO4, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 17, 2012
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 56.2 Å2
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.6 % / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1389)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PSN

4psn


Resolution: 2.9→29.932 Å / SU ML: 0.49 / σ(F): 1.99 / Phase error: 32.98 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3091 2322 5 %RANDOM
Rwork0.2672 ---
obs0.2693 46426 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→29.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13933 500 5 38 14476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414642
X-RAY DIFFRACTIONf_angle_d0.90919899
X-RAY DIFFRACTIONf_dihedral_angle_d12.4815661
X-RAY DIFFRACTIONf_chiral_restr0.0342380
X-RAY DIFFRACTIONf_plane_restr0.0042505
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8620X-RAY DIFFRACTION10.239TORSIONAL
12B8620X-RAY DIFFRACTION10.239TORSIONAL
13C8620X-RAY DIFFRACTION10.239TORSIONAL
14D8620X-RAY DIFFRACTION10.239TORSIONAL
15F8620X-RAY DIFFRACTION10.239TORSIONAL
16G8620X-RAY DIFFRACTION10.239TORSIONAL
17H8620X-RAY DIFFRACTION10.239TORSIONAL
18I8620X-RAY DIFFRACTION10.239TORSIONAL
21X52X-RAY DIFFRACTION10.239TORSIONAL
22Z52X-RAY DIFFRACTION10.239TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.95920.40631340.37472541X-RAY DIFFRACTION100
2.9592-3.02340.41481350.3632559X-RAY DIFFRACTION100
3.0234-3.09370.3651350.34212561X-RAY DIFFRACTION100
3.0937-3.1710.37251340.33792563X-RAY DIFFRACTION100
3.171-3.25660.35221350.32592548X-RAY DIFFRACTION100
3.2566-3.35230.34541360.30172591X-RAY DIFFRACTION100
3.3523-3.46040.36181350.29772557X-RAY DIFFRACTION100
3.4604-3.58390.31571360.28382584X-RAY DIFFRACTION100
3.5839-3.72710.35421350.27842564X-RAY DIFFRACTION100
3.7271-3.89640.29811360.2712587X-RAY DIFFRACTION100
3.8964-4.10130.29851350.26882569X-RAY DIFFRACTION100
4.1013-4.35760.30321360.2372586X-RAY DIFFRACTION100
4.3576-4.69280.28491380.22732629X-RAY DIFFRACTION100
4.6928-5.16290.25291380.22092608X-RAY DIFFRACTION100
5.1629-5.9050.27321380.24612622X-RAY DIFFRACTION100
5.905-7.42090.32071400.27792666X-RAY DIFFRACTION100
7.4209-29.9340.26011460.22092769X-RAY DIFFRACTION100

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