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- PDB-2p09: Structural Insights into the Evolution of a Non-Biological Protein -

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Basic information

Entry
Database: PDB / ID: 2p09
TitleStructural Insights into the Evolution of a Non-Biological Protein
Componentsa non-biological ATP binding protein with two mutations N32D and D65V
KeywordsDE NOVO PROTEIN / alpha/beta fold
Function / homologyNuclear Transport Factor 2; Chain: A, - #210 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / ADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / MAD / Resolution: 1.65 Å
AuthorsSmith, M. / Rosenow, M. / Wang, M. / Allen, J.P. / Szostak, J.W. / Chaput, J.C.
CitationJournal: PLoS ONE / Year: 2007
Title: Structural insights into the evolution of a non-biological protein: importance of surface residues in protein fold optimization.
Authors: Smith, M.D. / Rosenow, M.A. / Wang, M. / Allen, J.P. / Szostak, J.W. / Chaput, J.C.
History
DepositionFeb 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Feb 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 / pdbx_struct_special_symmetry / 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

Downloads & links

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Assembly

Deposited unit
A: a non-biological ATP binding protein with two mutations N32D and D65V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5545
Polymers9,7081
Non-polymers8464
Water1,982110
1
A: a non-biological ATP binding protein with two mutations N32D and D65V
hetero molecules

A: a non-biological ATP binding protein with two mutations N32D and D65V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,10910
Polymers19,4162
Non-polymers1,6938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4040 Å2
ΔGint-61 kcal/mol
Surface area8790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.791, 72.791, 54.752
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-300-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein a non-biological ATP binding protein with two mutations N32D and D65V


Mass: 9708.112 Da / Num. of mol.: 1 / Mutation: N32D,D65V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Non-polymers , 5 types, 114 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-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 4.31 Å3/Da / Density % sol: 71.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 250 mM sodium citrate, 100 mM sodium phosphate, 10 mM ATP, 300 mM sodium chloride, and 0.4-0.8% x/v polyethylene glycol 400, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionRedundancy: 5 % / Av σ(I) over netI: 17.5 / Number: 102082 / Rmerge(I) obs: 0.056 / Χ2: 1.26 / D res high: 1.65 Å / D res low: 50 Å / Num. obs: 20295 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.555099.710.0340.785
2.823.5599.910.0380.8375.2
2.462.8299.910.0621.1845.2
2.242.4699.810.0811.2655.2
2.082.2499.810.1061.1945.1
1.962.0899.410.1491.3445.1
1.861.9698.910.231.4865
1.781.8698.810.3121.514.9
1.711.789810.4441.5684.9
1.651.7196.910.5781.5584.7
ReflectionResolution: 1.65→50 Å / Num. obs: 20360 / % possible obs: 99.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.056 / Χ2: 1.305 / Net I/σ(I): 17.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.714.70.58619811.592196.9
1.71-1.784.90.45219761.614198
1.78-1.864.90.31520151.597198.8
1.86-1.9650.23419881.585198.9
1.96-2.085.10.15120211.351199.4
2.08-2.245.10.10620261.197199.8
2.24-2.465.20.08120561.284199.8
2.46-2.825.20.06220481.185199.9
2.82-3.555.20.03920740.881199.9
3.55-5050.03521750.892199.7

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Phasing

PhasingMethod: MAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
14.6744.90918.141S12.860.94
215.0126.03827.393S300.63
34.36640.32314.079S30.411.09
47.04128.75832.599S28.150.74
56.56142.97917.575S29.741.2
66.25747.05818.721S25.670.93
73.27744.29219.764S25.531.32
84.03345.10916.113S11.670.67
Phasing MR
Highest resolutionLowest resolution
Rotation1.91 Å27.32 Å
Translation1.91 Å27.32 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→27.32 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.176 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1044 5.1 %RANDOM
Rwork0.177 ---
obs0.177 20344 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.562 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.44 Å20 Å2
2--0.89 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.65→27.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms583 0 49 110 742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021651
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.999881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.117570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50923.22631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07815112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.806155
X-RAY DIFFRACTIONr_chiral_restr0.1450.288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02467
X-RAY DIFFRACTIONr_nbd_refined0.20.2285
X-RAY DIFFRACTIONr_nbtor_refined0.310.2419
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.216
X-RAY DIFFRACTIONr_mcbond_it1.2361.5357
X-RAY DIFFRACTIONr_mcangle_it2.022566
X-RAY DIFFRACTIONr_scbond_it3.2843350
X-RAY DIFFRACTIONr_scangle_it5.4964.5314
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 65 -
Rwork0.351 1407 -
obs-1472 97.42 %

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