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- PDB-4psl: Crystal structure of pfuThermo-DBP-RP1 (crystal form I) -

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Basic information

Entry
Database: PDB / ID: 4psl
TitleCrystal structure of pfuThermo-DBP-RP1 (crystal form I)
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 / MAD / Resolution: 3.5 Å
AuthorsGahlei, H. / von Moeller, H. / Eppers, D. / Sohmen, D. / Wilson, D.N. / 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 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4337
Polymers70,1454
Non-polymers2883
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13430 Å2
ΔGint-119 kcal/mol
Surface area30240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.636, 136.636, 122.055
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31B
41C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 2 - 145 / Label seq-ID: 3 - 146

Dom-IDAuth asym-IDLabel asym-ID
1AA
2DD
3BB
4CC

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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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 4.69 Å3/Da / Density % sol: 73.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 50 mM sodium cacodylate, pH 6.4, 2.3 M (NH4)2SO4 and 10 mM MgSO4, 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: 0.97962, 0.98003, 0.97185
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 21, 2009
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979621
20.980031
30.971851
ReflectionResolution: 3.5→35 Å / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 69.5 Å2
Reflection shellResolution: 3.5→3.85 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.5→34.16 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.902 / SU B: 65.856 / SU ML: 0.454 / Cross valid method: THROUGHOUT / ESU R Free: 0.53 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26693 820 5 %RANDOM
Rwork0.20718 ---
obs0.21015 15568 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 118.651 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20.86 Å20 Å2
2--1.73 Å20 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 3.5→34.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4798 0 15 31 4844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224862
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9966490
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8015586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25725.242227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.5151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5331532
X-RAY DIFFRACTIONr_chiral_restr0.0680.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023464
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3811.52926
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.77224724
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.28531936
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0934.51766
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1172 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.540.5
Bmedium positional0.60.5
Cmedium positional0.560.5
Dmedium positional0.540.5
Amedium thermal0.282
Bmedium thermal0.282
Cmedium thermal0.312
Dmedium thermal0.262
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 61 -
Rwork0.273 1148 -
obs--100 %
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)
14.1954-3.1827-1.28022.93870.60311.52130.3757-0.6630.8574-0.15780.1704-0.6108-0.13220.4406-0.54610.1838-0.118-0.03880.4572-0.18870.34959.6701-67.839715.8798
22.6409-1.8107-1.20953.69380.5982.07530.1807-0.13810.1764-0.07830.19040.0738-0.186-0.0793-0.3710.2309-0.06980.14350.1444-0.06530.15999.0329-65.5458-8.5194
35.2702-3.5374-1.90093.17971.96731.38710.4784-0.3881.0488-0.2806-0.0283-0.6805-0.2470.0426-0.45010.506-0.18220.47760.2671-0.15380.5324-22.9645-35.078620.6988
45.103-3.5491-1.93143.52471.89311.29531.33561.11411.2584-1.3059-0.7808-0.5491-0.8614-0.5267-0.55481.09480.39770.66450.57180.46650.8261-22.6591-31.0961-3.8177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 148
2X-RAY DIFFRACTION2B1 - 147
3X-RAY DIFFRACTION3C1 - 148
4X-RAY DIFFRACTION4D1 - 148

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