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- PDB-3dgn: A non-biological ATP binding protein crystallized in the presence... -

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Basic information

Entry
Database: PDB / ID: 3dgn
TitleA non-biological ATP binding protein crystallized in the presence of 100 mM ADP
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'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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)10,4135
Polymers9,7081
Non-polymers7054
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.383, 72.383, 54.777
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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 4.38 Å3/Da / Density % sol: 71.9 %
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: Feb 21, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 4736 / % possible obs: 99.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.283 / Χ2: 3.388 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.7-2.86.54692.44399.8
2.8-2.916.54732.5551000.964
2.91-3.046.34752.6351000.635
3.04-3.26.64632.9561000.522
3.2-3.46.64592.9299.60.421
3.4-3.666.34733.61299.20.348
3.66-4.036.64705.08699.60.252
4.03-4.616.54735.4598.50.207
4.61-5.86.64793.13598.80.177
5.8-256.45023.046960.112

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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: 2.7→23.7 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.861 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.649 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.325 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 215 4.6 %RANDOM
Rwork0.197 ---
obs0.2 4720 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.22 Å2 / Biso mean: 27.778 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å2-0 Å2
2--0.1 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.7→23.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms587 0 42 33 662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.021644
X-RAY DIFFRACTIONr_angle_refined_deg2.9551.986870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.504570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.09523.22631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19315112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.264155
X-RAY DIFFRACTIONr_chiral_restr0.1960.288
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021467
X-RAY DIFFRACTIONr_mcbond_it1.1481.5347
X-RAY DIFFRACTIONr_mcangle_it2.1692566
X-RAY DIFFRACTIONr_scbond_it3.7043297
X-RAY DIFFRACTIONr_scangle_it6.1134.5303
LS refinement shellResolution: 2.7→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.56 11 -
Rwork0.303 344 -
all-355 -
obs--100 %

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