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- PDB-4psn: Crystal structure of apeThermo-DBP-RP2 -

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Basic information

Entry
Database: PDB / ID: 4psn
TitleCrystal structure of apeThermo-DBP-RP2
ComponentsssDNA binding protein
KeywordsDNA BINDING PROTEIN / ssDNA binding protein
Function / homology: / Thermo-DBP-RP2 C-terminal domain / ThermoDBP-related, archaea / ThermoDBP-related, archaea / IMIDAZOLE / Thermo-DBP-RP2-like C-terminal domain-containing protein
Function and homology information
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 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 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,67112
Polymers107,0724
Non-polymers5998
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19690 Å2
ΔGint-25 kcal/mol
Surface area39140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.240, 108.640, 154.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ssDNA binding protein


Mass: 26768.100 Da / Num. of mol.: 4
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: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M imidazole, pH 8.0, 0.4 M NaH2PO4, 1.6 M K2HPO4, 0.2 M NaCl and 0.25 M glycine, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 7, 2010
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 125145 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 28.8 Å2
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 5.9 % / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
HKL2Mapmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→32.727 Å / SU ML: 0.25 / Phase error: 20.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 3207 5.05 %RANDOM
Rwork0.1793 ---
obs0.1811 63466 96.71 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.614 Å2 / ksol: 0.419 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6062 Å20 Å2-0 Å2
2--5.1365 Å20 Å2
3----3.5303 Å2
Refinement stepCycle: LAST / Resolution: 2.05→32.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6995 0 42 283 7320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087200
X-RAY DIFFRACTIONf_angle_d1.0829741
X-RAY DIFFRACTIONf_dihedral_angle_d14.9072765
X-RAY DIFFRACTIONf_chiral_restr0.0721161
X-RAY DIFFRACTIONf_plane_restr0.0041272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.08060.29841360.24182445X-RAY DIFFRACTION93
2.0806-2.11310.2651530.19022456X-RAY DIFFRACTION92
2.1131-2.14770.24021230.17712478X-RAY DIFFRACTION93
2.1477-2.18480.21911520.18192531X-RAY DIFFRACTION95
2.1848-2.22450.241310.18632507X-RAY DIFFRACTION93
2.2245-2.26730.26971160.21442393X-RAY DIFFRACTION89
2.2673-2.31350.22071260.17862521X-RAY DIFFRACTION94
2.3135-2.36380.26331370.17812559X-RAY DIFFRACTION96
2.3638-2.41880.24851230.19632601X-RAY DIFFRACTION97
2.4188-2.47930.26691500.1892589X-RAY DIFFRACTION97
2.4793-2.54630.25451450.1912601X-RAY DIFFRACTION97
2.5463-2.62120.25291330.18242615X-RAY DIFFRACTION97
2.6212-2.70570.21521320.1852639X-RAY DIFFRACTION97
2.7057-2.80240.23531520.19052639X-RAY DIFFRACTION98
2.8024-2.91450.22451530.18462687X-RAY DIFFRACTION99
2.9145-3.04710.23241540.18152656X-RAY DIFFRACTION99
3.0471-3.20760.22341330.17172715X-RAY DIFFRACTION99
3.2076-3.40840.17211570.16312683X-RAY DIFFRACTION100
3.4084-3.67120.19041350.16512709X-RAY DIFFRACTION100
3.6712-4.04010.19751260.1642759X-RAY DIFFRACTION100
4.0401-4.62330.17991380.15332772X-RAY DIFFRACTION100
4.6233-5.81950.19731370.17882792X-RAY DIFFRACTION100
5.8195-32.73130.21251650.20482912X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.3485 Å / Origin y: -15.9074 Å / Origin z: 38.1118 Å
111213212223313233
T0.0743 Å2-0.0043 Å2-0.0019 Å2-0.0854 Å2-0.0051 Å2--0.0809 Å2
L0.1888 °20.0002 °2-0.2771 °2-0.1262 °20.0767 °2--0.4232 °2
S0.0106 Å °0.013 Å °-0.0004 Å °0.0149 Å °0.0025 Å °0.0045 Å °0.0217 Å °-0.0359 Å °-0.0068 Å °
Refinement TLS groupSelection details: all

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