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- PDB-4psm: Crystal structure of pfuThermo-DBP-RP1 (crystal form II) -

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Basic information

Entry
Database: PDB / ID: 4psm
TitleCrystal structure of pfuThermo-DBP-RP1 (crystal form II)
ComponentsssDNA binding protein
KeywordsDNA BINDING PROTEIN / ssDNA binding protein
Function / homologyThermoDBP-related, archaea / ThermoDBP-related, archaea / DUF2258 domain-containing protein
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)70,5308
Polymers70,1454
Non-polymers3844
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13920 Å2
ΔGint-123 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.251, 199.303, 114.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 3:148 )
211chain B and (resseq 3:148 )
311chain C and (resseq 3:148 )
411chain D and (resseq 3:148 )

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Components

#1: Protein
ssDNA binding protein


Mass: 17536.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1044 / Plasmid: pET-M11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q8U208
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 0.2 M Li2SO4 and 40 % (v/v) PEG400, 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: 1.0385 Å
DetectorType: RAYONIX MX-225 / Detector: CCD
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0385 Å / Relative weight: 1
ReflectionResolution: 2.43→35 Å / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 37.5 Å2
Reflection shellResolution: 2.43→2.49 Å / Redundancy: 5.7 % / % possible all: 98.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PSL

4psl


Resolution: 2.43→33.409 Å / SU ML: 0.33 / σ(F): 2 / Phase error: 34.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 1335 5 %RANDOM
Rwork0.2226 ---
obs0.2253 26694 98.97 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.757 Å2 / ksol: 0.401 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.4986 Å20 Å2-0 Å2
2--2.9481 Å20 Å2
3----18.4467 Å2
Refinement stepCycle: LAST / Resolution: 2.43→33.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4778 0 20 68 4866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054864
X-RAY DIFFRACTIONf_angle_d0.9926493
X-RAY DIFFRACTIONf_dihedral_angle_d16.0451943
X-RAY DIFFRACTIONf_chiral_restr0.119729
X-RAY DIFFRACTIONf_plane_restr0.002819
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1180X-RAY DIFFRACTIONPOSITIONAL
12B1180X-RAY DIFFRACTIONPOSITIONAL0.049
13C1185X-RAY DIFFRACTIONPOSITIONAL0.074
14D1197X-RAY DIFFRACTIONPOSITIONAL0.062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.51690.36461310.26672481X-RAY DIFFRACTION99
2.5169-2.61760.44351300.29032501X-RAY DIFFRACTION99
2.6176-2.73670.33691320.25842509X-RAY DIFFRACTION99
2.7367-2.88090.31361330.24012522X-RAY DIFFRACTION100
2.8809-3.06130.29011330.24242530X-RAY DIFFRACTION99
3.0613-3.29740.341320.21362514X-RAY DIFFRACTION99
3.2974-3.62890.27341340.22912530X-RAY DIFFRACTION99
3.6289-4.15320.24381330.18392556X-RAY DIFFRACTION99
4.1532-5.22930.25021370.1942584X-RAY DIFFRACTION99
5.2293-33.41220.21841400.23192632X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 7.939 Å / Origin y: 49.7441 Å / Origin z: -13.9703 Å
111213212223313233
T0.022 Å20.0122 Å2-0.0221 Å2--0.01 Å20.0755 Å2--0.5604 Å2
L1.0841 °2-1.4108 °2-0.0697 °2-1.9112 °20.0677 °2--0.1545 °2
S-0.0328 Å °0.0173 Å °0.0219 Å °-0.0032 Å °0.0377 Å °0.175 Å °-0.0522 Å °-0.0169 Å °0.002 Å °
Refinement TLS groupSelection details: all

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