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- PDB-3dgo: A non-biological ATP binding protein with a Tyr-Phe mutation in t... -

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Basic information

Entry
Database: PDB / ID: 3dgo
TitleA non-biological ATP binding protein with a Tyr-Phe mutation in the ligand binding domain
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: 2.5 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

Downloads & links

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Assembly

Deposited unit
A: ATP Binding Protein-DX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6197
Polymers9,6921
Non-polymers9266
Water55831
1
A: ATP Binding Protein-DX
hetero molecules

A: ATP Binding Protein-DX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,23714
Polymers19,3842
Non-polymers1,85312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area4630 Å2
ΔGint-52 kcal/mol
Surface area8980 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.742, 71.742, 55.488
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ATP Binding Protein-DX


Mass: 9692.112 Da / Num. of mol.: 1 / Mutation: Y43F
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)

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Non-polymers , 5 types, 37 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


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


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


Mass: 18.015 Da / Num. of mol.: 31 / 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: 4.36 Å3/Da / Density % sol: 71.81 %
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: May 7, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 5940 / % possible obs: 99.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.084 / Χ2: 3.538 / Net I/σ(I): 18.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.595.20.6255843.043100
2.59-2.695.20.475713.05299.8
2.69-2.825.40.3775934.206100
2.82-2.965.40.2485893.71699.8
2.96-3.155.60.1775794.16599.7
3.15-3.395.80.1165943.94299.8
3.39-3.735.80.0825893.52100
3.73-4.275.80.0596113.649100
4.27-5.375.90.0485963.04399.5
5.37-255.60.046343.02898.4

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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: 2.5→23.49 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.068 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 267 4.5 %RANDOM
Rwork0.184 ---
obs0.186 5934 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.59 Å2 / Biso mean: 42.155 Å2 / Biso min: 17.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å2-0 Å2
2--0.05 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→23.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms582 0 54 31 667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021648
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210
X-RAY DIFFRACTIONr_angle_refined_deg2.2981.998871
X-RAY DIFFRACTIONr_angle_other_deg1.015322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.079568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4723.22631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39315111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.388155
X-RAY DIFFRACTIONr_chiral_restr0.1320.286
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021462
X-RAY DIFFRACTIONr_mcbond_it1.1181.5344
X-RAY DIFFRACTIONr_mcangle_it2.1942559
X-RAY DIFFRACTIONr_scbond_it3.823304
X-RAY DIFFRACTIONr_scangle_it6.4854.5312
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 22 -
Rwork0.281 400 -
all-422 -
obs--98.6 %

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