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- PDB-10on: crystal form two of the Roseophage RDJLF1 GapR -

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Basic information

Entry
Database: PDB / ID: 10on
Titlecrystal form two of the Roseophage RDJLF1 GapR
ComponentsGapR-like DNA-binding domain-containing protein
KeywordsVIRAL PROTEIN / NAP / nucleoid associated protein / GapR / phage / RDJLF1 / NAP poison
Function / homologyGapR-like, DNA-binding domain / GapR-like, DNA-binding domain / DNA binding / GapR-like DNA-binding domain-containing protein
Function and homology information
Biological speciesRoseobacter phage RDJL Phi 1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSchumacher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: To Be Published
Title: crystal form two of the Roseophage RDJLF1 GapR
Authors: Schumacher, M.A.
History
DepositionJan 29, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: GapR-like DNA-binding domain-containing protein
A: GapR-like DNA-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2684
Polymers19,0762
Non-polymers1922
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-63 kcal/mol
Surface area9020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.774, 48.774, 182.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein GapR-like DNA-binding domain-containing protein


Mass: 9537.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseobacter phage RDJL Phi 1 (virus) / Gene: RDJLphi1_gp30 / Production host: Escherichia coli (E. coli) / References: UniProt: F4YXP1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.84 Å3/Da / Density % sol: 56.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 50 mM sodium cacodylate pH 6.0, 2 mM CaCl2, 1.8 M ammonium sulphate, 0.5 mM spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→47.12 Å / Num. obs: 4753 / % possible obs: 98.1 % / Redundancy: 9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.031 / Net I/σ(I): 20.2
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 445 / CC1/2: 0.995 / Rpim(I) all: 0.055

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→47.12 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2716 475 10 %
Rwork0.2231 --
obs0.2283 4751 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 10 21 1213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071202
X-RAY DIFFRACTIONf_angle_d1.0131614
X-RAY DIFFRACTIONf_dihedral_angle_d13.863464
X-RAY DIFFRACTIONf_chiral_restr0.053174
X-RAY DIFFRACTIONf_plane_restr0.011218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.430.34551490.26251346X-RAY DIFFRACTION95
3.43-4.330.27161570.21161413X-RAY DIFFRACTION98
4.33-47.120.24351690.21541517X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 14.1631 Å / Origin y: 13.7094 Å / Origin z: 10.5061 Å
111213212223313233
T0.3149 Å2-0.0299 Å20.0279 Å2-0.3022 Å20.0071 Å2--0.2848 Å2
L4.6319 °2-4.2571 °20.9554 °2-4.2194 °2-0.8954 °2--1.2131 °2
S0.3173 Å °0.3361 Å °0.1746 Å °-0.2929 Å °-0.3458 Å °-0.1987 Å °0.0609 Å °0.098 Å °0.0321 Å °
Refinement TLS groupSelection details: all

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