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- PDB-6cfy: Bosea sp Root 381 apo GapR structure -

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Basic information

Entry
Database: PDB / ID: 6cfy
TitleBosea sp Root 381 apo GapR structure
ComponentsUPF0335 protein ASE63_04290
KeywordsDNA BINDING PROTEIN / Caulobacter / NAP / DNA binding / topoisomerase
Function / homologyGapR-like / GapR-like, DNA-binding domain / GapR-like, DNA-binding domain / DNA binding / UPF0335 protein ASE63_04290
Function and homology information
Biological speciesBosea sp. Root381 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSchumacherr, 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 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0335 protein ASE63_04290


Theoretical massNumber of molelcules
Total (without water)9,2881
Polymers9,2881
Non-polymers00
Water905
1
A: UPF0335 protein ASE63_04290

A: UPF0335 protein ASE63_04290


Theoretical massNumber of molelcules
Total (without water)18,5762
Polymers18,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2430 Å2
ΔGint-19 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.589, 39.589, 205.125
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein UPF0335 protein ASE63_04290


Mass: 9287.882 Da / Num. of mol.: 1 / Mutation: L48M, I54M, L73M
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 4.85 Å3/Da / Density % sol: 74.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 15% MPD, 10 mM MgCl2, HEPES (7.5) 0.001 M spermine

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→38.87 Å / Num. obs: 12187 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 0.997 / Rpim(I) all: 0.041 / Rrim(I) all: 0.122 / Rsym value: 0.099 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.53 Å / Num. unique obs: 1213 / CC1/2: 0.319 / % possible all: 99.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→38.8 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0.79 / Phase error: 22.03
RfactorNum. reflection% reflection
Rfree0.2659 1235 10.13 %
Rwork0.231 --
obs0.2344 12187 99.95 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 81.292 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 140.06 Å2 / Biso mean: 69.35 Å2 / Biso min: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.4118 Å20 Å2-0 Å2
2--3.4118 Å20 Å2
3----6.8237 Å2
Refinement stepCycle: final / Resolution: 2.4→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms567 0 0 5 572
Biso mean---64.25 -
Num. residues----70
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018569
X-RAY DIFFRACTIONf_angle_d1.675757
X-RAY DIFFRACTIONf_chiral_restr0.10384
X-RAY DIFFRACTIONf_plane_restr0.00799
X-RAY DIFFRACTIONf_dihedral_angle_d15.75233
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4001-2.49620.34651390.332912131352
2.4962-2.60980.37481370.340112201357
2.6098-2.74740.3211350.292612031338
2.7474-2.91940.28411350.257212291364
2.9194-3.14480.26821400.213912141354
3.1448-3.4610.28181360.191212031339
3.461-3.96140.27331380.210612521390
3.9614-4.98930.22531380.181612091347
4.9893-38.87670.26131370.273112091346
Refinement TLS params.Method: refined / Origin x: -0.8545 Å / Origin y: -16.4547 Å / Origin z: 9.7667 Å
111213212223313233
T0.388 Å20.0051 Å2-0.0771 Å2-0.5721 Å2-0.0266 Å2--0.4802 Å2
L0.1954 °20.133 °20.2328 °2-0.2181 °20.152 °2--0.2481 °2
S0.0276 Å °-0.1724 Å °0.0089 Å °0.1206 Å °-0.045 Å °0.0479 Å °-0.0361 Å °0.2061 Å °0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 78
2X-RAY DIFFRACTION1allS1 - 5

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