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- PDB-3dgl: 1.8 A Crystal Structure of a Non-biological Protein with Bound AT... -

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Basic information

Entry
Database: PDB / ID: 3dgl
Title1.8 A Crystal Structure of a Non-biological Protein with Bound ATP in a Novel Bent Conformation
ComponentsATP Binding Protein-DX
KeywordsDE NOVO PROTEIN / alpha/beta fold / bent ATP / non-biological protein
Function / homologyNuclear Transport Factor 2; Chain: A, - #210 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSimmons, C.R. / Allen, J.P. / Chaput, J.C.
CitationJournal: Acs Chem.Biol. / Year: 2009
Title: A synthetic protein selected for ligand binding affinity mediates ATP hydrolysis.
Authors: Simmons, C.R. / Stomel, J.M. / McConnell, M.D. / Smith, D.A. / Watkins, J.L. / Allen, J.P. / Chaput, J.C.
History
DepositionJun 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: ATP Binding Protein-DX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5996
Polymers9,7081
Non-polymers8915
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.702, 73.702, 54.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ATP Binding Protein-DX


Mass: 9708.112 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: pIADL14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 4.54 Å3/Da / Density % sol: 72.89 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 8.5
Details: 0.1 M sodium phosphate, 0.25 M sodium citrate, 0.3 M sodium chloride, 23% polyethylene glycol 400, 0.2 M ammonium acetate, pH 8.5, sitting drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 143 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 15, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 16220 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.069 / Χ2: 2.334 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.8612.50.44515922.119100
1.86-1.9412.60.34916022.352100
1.94-2.0312.70.26716062.364100
2.03-2.1312.80.17915972.51100
2.13-2.2712.90.14415982.601100
2.27-2.4412.90.11616162.498100
2.44-2.6913.10.09316202.405100
2.69-3.0813.20.06216262.324100
3.08-3.8713.20.04216462.247100
3.87-2512.70.03117171.941100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
REFMAC5.4.0066refinement
PDB_EXTRACT3.006data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.57 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 815 5 %RANDOM
Rwork0.172 ---
obs0.173 16214 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.24 Å2 / Biso mean: 24.359 Å2 / Biso min: 11.01 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms588 0 53 149 790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021655
X-RAY DIFFRACTIONr_angle_refined_deg1.4232883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.558570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33923.43832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71915112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.424155
X-RAY DIFFRACTIONr_chiral_restr0.0950.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021471
X-RAY DIFFRACTIONr_mcbond_it0.831.5347
X-RAY DIFFRACTIONr_mcangle_it1.5752565
X-RAY DIFFRACTIONr_scbond_it2.2523308
X-RAY DIFFRACTIONr_scangle_it3.6724.5317
LS refinement shellResolution: 1.8→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 49 -
Rwork0.219 1122 -
all-1171 -
obs--99.66 %

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