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- PDB-3lt9: A non-biological ATP binding protein with a single point mutation... -

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Basic information

Entry
Database: PDB / ID: 3lt9
TitleA non-biological ATP binding protein with a single point mutation (D65V), that contributes to optimized folding and ligand binding
ComponentsATP BINDING PROTEIN-D65V
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 / MOLECULAR REPLACEMENT / Resolution: 2.55 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 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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-D65V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5547
Polymers9,7071
Non-polymers8466
Water55831
1
A: ATP BINDING PROTEIN-D65V
hetero molecules

A: ATP BINDING PROTEIN-D65V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,10714
Polymers19,4142
Non-polymers1,69312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5120 Å2
ΔGint-49 kcal/mol
Surface area8390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.461, 71.461, 55.583
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-D65V


Mass: 9707.128 Da / Num. of mol.: 1 / Mutation: D65V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Description: THE ATP BINDING PROTEIN CONSTRUCT WAS DERIVED DE NOVO VIA DIRECTED EVOLUTION
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-ADP / ADENOSINE-5'-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


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#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.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE D65V MUTATION IS WITH RESPECT TO THE SEQUENCE GIVEN FOR PDB ENTRY 2P05

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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: 4.22 Å3/Da / Density % sol: 70.86 %
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
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2817 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 5562 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 25.481
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.494 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G4B

3g4b
PDB Unreleased entry


Resolution: 2.55→41.34 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.89 / SU B: 6.685 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.239 251 4.5 %RANDOM
Rwork0.178 ---
obs0.181 5558 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.55→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms583 0 50 31 664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021645
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.711.989866
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.412568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66123.22631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14415111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.925155
X-RAY DIFFRACTIONr_chiral_restr0.1120.286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021463
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_it0.7731.5344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5472559
X-RAY DIFFRACTIONr_scbond_it2.4983301
X-RAY DIFFRACTIONr_scangle_it4.3564.5307
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 20 -
Rwork0.236 374 -
obs--100 %

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