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- PDB-3ltd: X-ray structure of a non-biological ATP binding protein determine... -

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Basic information

Entry
Database: PDB / ID: 3ltd
TitleX-ray structure of a non-biological ATP binding protein determined at 2.8 A by multi-wavelength anomalous dispersion
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 speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsSimmons, C.R. / Magee, C.L. / Allen, J.P. / Chaput, J.C.
CitationJournal: Biochemistry / Year: 2010
Title: Three-dimensional structures reveal multiple ADP/ATP binding modes for a synthetic class of artificial proteins.
Authors: Simmons, C.R. / Magee, C.L. / Smith, D.A. / Lauman, L. / Chaput, J.C. / Allen, J.P.
History
DepositionFeb 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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)10,4486
Polymers9,7081
Non-polymers7405
Water27015
1
A: ATP BINDING PROTEIN-DX
hetero molecules

A: ATP BINDING PROTEIN-DX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,89712
Polymers19,4162
Non-polymers1,48110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4390 Å2
ΔGint-40 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.145, 73.145, 54.804
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 9708.112 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Description: THE CONSTRUCT IS A NON-BIOLOGICAL ATP BINDING PROTEIN THAT WAS DISCOVERED THROUGH DIRECTED EVOLUTION.
Plasmid: PIADL14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Non-polymers , 5 types, 20 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 71.78 %
Description: The Structure Factor File contains Friedel pairs
Crystal growpH: 8.5
Details: 0.1 M SODIUM PHOSPHATE PH 8.5, 0.25 M SODIUM CITRATE, 0.3 M SODIUM CHLORIDE, 23% PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.2817, 1.2750, 1.2822
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2008
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28171
21.2751
31.28221
ReflectionResolution: 2.8→50 Å / Num. obs: 4054 / % possible obs: 92.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 12.69
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.505 / % possible all: 94.3

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→36.56 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.14 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE FRIEDEL PAIRS WERE USED IN PHASING. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 188 4.6 %RANDOM
Rwork0.18 ---
obs0.182 4053 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å2-0 Å2
2--0.07 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms583 0 43 15 641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021639
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.986861
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.062568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4923.22631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14315111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.198155
X-RAY DIFFRACTIONr_chiral_restr0.0990.286
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021463
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6461.5344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.282559
X-RAY DIFFRACTIONr_scbond_it2.0783295
X-RAY DIFFRACTIONr_scangle_it3.5994.5302
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 16 -
Rwork0.258 278 -
obs--94.23 %

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