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- PDB-6cfx: Bosea sp GapR solved in the presence of DNA -

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Basic information

Entry
Database: PDB / ID: 6cfx
TitleBosea sp GapR solved in the presence of DNA
ComponentsUPF0335 protein ASE63_04290
KeywordsDNA BINDING PROTEIN / Caulobacter / DNA binding / NAP / DNA twist
Function / homologyGapR-like / GapR-like, DNA-binding domain / GapR-like, DNA-binding domain / DNA binding / PHOSPHATE ION / UPF0335 protein ASE63_04290
Function and homology information
Biological speciesBosea sp. Root381 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSchumacher, M.A.
CitationJournal: Cell / Year: 2018
Title: A Bacterial Chromosome Structuring Protein Binds Overtwisted DNA to Stimulate Type II Topoisomerases and Enable DNA Replication.
Authors: Guo, M.S. / Haakonsen, D.L. / Zeng, W. / Schumacher, M.A. / Laub, M.T.
History
DepositionFeb 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0335 protein ASE63_04290
B: UPF0335 protein ASE63_04290
C: UPF0335 protein ASE63_04290
D: UPF0335 protein ASE63_04290
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3756
Polymers36,1854
Non-polymers1902
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-86 kcal/mol
Surface area18340 Å2
MethodPISA
2
A: UPF0335 protein ASE63_04290
B: UPF0335 protein ASE63_04290
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1873
Polymers18,0922
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-23 kcal/mol
Surface area11380 Å2
MethodPISA
3
A: UPF0335 protein ASE63_04290
C: UPF0335 protein ASE63_04290
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1873
Polymers18,0922
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-15 kcal/mol
Surface area12130 Å2
MethodPISA
4
B: UPF0335 protein ASE63_04290
D: UPF0335 protein ASE63_04290
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1873
Polymers18,0922
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-15 kcal/mol
Surface area12440 Å2
MethodPISA
5
C: UPF0335 protein ASE63_04290
D: UPF0335 protein ASE63_04290
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1873
Polymers18,0922
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-25 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.328, 44.483, 107.051
Angle α, β, γ (deg.)90.000, 101.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
UPF0335 protein ASE63_04290


Mass: 9046.187 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bosea sp. Root381 (bacteria) / Gene: ASE63_04290 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q9HY32
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: ammonium sulphate, MES buffer pH 6.5

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50.24 Å / Num. obs: 29676 / % possible obs: 92 % / Observed criterion σ(F): 0 / Redundancy: 2.5 % / CC1/2: 0.994 / Rpim(I) all: 0.042 / Rrim(I) all: 0.072 / Rsym value: 0.059 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1921 / CC1/2: 0.975 / Rpim(I) all: 0.0105 / Rrim(I) all: 0.0174 / Rsym value: 0.0137 / % possible all: 69.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CG8

6cg8


Resolution: 2→50.24 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.05
RfactorNum. reflection% reflection
Rfree0.222 2010 6.77 %
Rwork0.1985 --
obs0.2001 29676 91.69 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 51.82 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso max: 119.75 Å2 / Biso mean: 38.24 Å2 / Biso min: 9.86 Å2
Baniso -1Baniso -2Baniso -3
1--3.0987 Å20 Å20.6938 Å2
2--7.6529 Å20 Å2
3----4.5541 Å2
Refinement stepCycle: final / Resolution: 2→50.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 10 341 2748
Biso mean--32.9 42.58 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032427
X-RAY DIFFRACTIONf_angle_d0.5043253
X-RAY DIFFRACTIONf_chiral_restr0.034370
X-RAY DIFFRACTIONf_plane_restr0.001430
X-RAY DIFFRACTIONf_dihedral_angle_d14.297967
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.07160.29591390.20881921206064
2.0716-2.15450.22381750.19272421259681
2.1545-2.25260.26952020.21562865306795
2.2526-2.37130.22912120.19962874308696
2.3713-2.51990.25992080.1912877308596
2.5199-2.71440.22282170.19822928314597
2.7144-2.98760.2352100.20762912312297
2.9876-3.41980.2172150.19932925314096
3.4198-4.30820.18892090.17462942315197
4.3082-50.25550.21552230.2133001322496
Refinement TLS params.Method: refined / Origin x: 17.2251 Å / Origin y: 0.2868 Å / Origin z: 25.4108 Å
111213212223313233
T0.1331 Å2-0.0206 Å2-0.0015 Å2-0.092 Å20.0012 Å2--0.1304 Å2
L0.5276 °2-0.045 °2-0.0718 °2-0.0779 °20.2154 °2--0.6578 °2
S0.0172 Å °-0.1168 Å °0.0006 Å °0.0204 Å °-0.0564 Å °0.0138 Å °0.0029 Å °-0.0044 Å °0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 78
2X-RAY DIFFRACTION1allB5 - 78
3X-RAY DIFFRACTION1allC3 - 78
4X-RAY DIFFRACTION1allD3 - 80
5X-RAY DIFFRACTION1allW833 - 834
6X-RAY DIFFRACTION1allS1 - 349

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