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- PDB-1uw1: A Novel ADP- and Zinc-binding fold from function-directed in vitr... -

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Basic information

Entry
Database: PDB / ID: 1uw1
TitleA Novel ADP- and Zinc-binding fold from function-directed in vitro evolution
ComponentsARTIFICIAL NUCLEOTIDE BINDING PROTEIN (ANBP)
KeywordsDE NOVO PROTEIN / ARTIFICIAL NUCLEOTIDE BINDING PROTEIN / NUCLEOTIDE BINDING PROTEIN / IN VITRO EVOLUTION
Function / homologyNuclear Transport Factor 2; Chain: A, - #210 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / ADENOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å
AuthorsLo Surdo, P. / Walsh, M.A. / Sollazzo, M.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: A Novel Adp- and Zinc-Binding Fold from Function-Directed in Vitro Evolution
Authors: Lo Surdo, P. / Walsh, M.A. / Sollazzo, M.
#1: Journal: Nature / Year: 2001
Title: Functional Proteins from a Random Sequence Library
Authors: Keefe, A.D. / Szostak, J.W.
History
DepositionJan 28, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARTIFICIAL NUCLEOTIDE BINDING PROTEIN (ANBP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0993
Polymers9,6061
Non-polymers4932
Water1,78399
1
A: ARTIFICIAL NUCLEOTIDE BINDING PROTEIN (ANBP)
hetero molecules

A: ARTIFICIAL NUCLEOTIDE BINDING PROTEIN (ANBP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1976
Polymers19,2122
Non-polymers9854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area2590 Å2
ΔGint-13 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.077, 71.077, 54.883
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-2090-

HOH

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Components

#1: Protein ARTIFICIAL NUCLEOTIDE BINDING PROTEIN (ANBP)


Mass: 9605.979 Da / Num. of mol.: 1 / Fragment: NUCLEOTIDE BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: THIS IS A RANDOMLY GENERATED PROTEIN. THE PROTEIN WAS ISOLATED BY CYCLES OF IN VITRO EVOLUTIONARY SELECTION, FROM A RANDOM-SEQUENCE LIBRARY OF 6 X 10**12 MRNA-DISPLAYED PROTEINS. EVOLUTION ...Details: THIS IS A RANDOMLY GENERATED PROTEIN. THE PROTEIN WAS ISOLATED BY CYCLES OF IN VITRO EVOLUTIONARY SELECTION, FROM A RANDOM-SEQUENCE LIBRARY OF 6 X 10**12 MRNA-DISPLAYED PROTEINS. EVOLUTION OF THE PROTEINS PRODUCED WAS DIRECTED BY THE ABILITY TO BIND ATP
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: SYNTHETIC GENE / Plasmid: MODIFIED PET-24D WITH N-HIS-TEV CLEAVAGE SITE / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
#2: 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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ORIGINAL FUNCTIONAL PROTEIN ISOLATED BY KEEFE AND SZOSTAK (NCBI: AAK50879, GI:13958624) ...THE ORIGINAL FUNCTIONAL PROTEIN ISOLATED BY KEEFE AND SZOSTAK (NCBI: AAK50879, GI:13958624) CONSISTED OF 109 AMINO ACID RESIDUES.A SERIES OF CONSTRUCTS WERE PRODUCED TO IDENTIFY THE FUNCTIONAL CORE OF THE PROTEIN TO AID STRUCTURAL STUDIES. THIS IS A RANDOMLY GENERATED PROTEIN. THE PROTEON WAS ISOLATED BY CYCLES OF IN VITRO EVOLUTIONARY SELECTION FROM A RANDOM-SEQUENCE LIBRARY OF 6 X 10**12 MRNA-DISPLAYED PROTEINS. EVOLUTION OF THE PROTEINS PRODUCED WAS DIRECTED BY THE ABILITY TO BIND ATP.
Sequence detailsTHE ORIGINAL FUNCTIONAL PROTEIN ISOLATED BY KEEFE AND SZOSTAK (NCBI: AAK50879, GI:13958624) ...THE ORIGINAL FUNCTIONAL PROTEIN ISOLATED BY KEEFE AND SZOSTAK (NCBI: AAK50879, GI:13958624) CONSISTED OF 109 AMINO ACID RESIDUES.A SERIES OF CONSTRUCTS WERE PRODUCED TO IDENTIFY THE FUNCTIONAL CORE OF THE PROTEIN TO AID STRUCTURAL STUDIES. THIS ENTRY CORRESPONDS TO CONSTRUCT REFERRED TO AS ANBP. THE ANBP CONSTRUCT CONSISTS OF RESIDUES 1-78 WHICH WAS EXPRESSED WITH AN N-TERMINAL 6-HIS TAG THAT WAS REMOVED BY CLEAVAGE WITH TEV PROTEASE BEFORE BEING CRYSTALLIZED. THIS GIVES AN INSERTION OF TWO RESIDUES, GA, AT THE N-TER). THIS IS A RANDOMLY GENERATED PROTEIN. THE PROTEON WAS ISOLATED BY CYCLES OF IN VITRO EVOLUTIONARY SELECTION FROM A RANDOM-SEQUENCE LIBRARY OF 6 X 10**12 MRNA-DISPLAYED PROTEINS. EVOLUTION OF THE PROTEINS PRODUCED WAS DIRECTED BY THE ABILITY TO BIND ATP. THERE IS NO UNIPROT ID ASSOCIATED WITH THE SEQUENCE PRESENT IN THIS ENTRY AND THEREFORE, THE DBREF RECORDS INDICATE THAT THE SEQUENCE IS MAPPED TO ITSELF.

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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: 4.4 Å3/Da / Density % sol: 72.1 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: USING THE HANGING-DROP VAPOR DIFFUSION TECHIQUE. 20MG/ML OF PROTEIN WAS MIXED IN EQUAL VOLUMES WITH A CRYSTALLIZATION BUFFER OF 0.1M TRIS/HCL PH 8.5, 0.2 M SODIUM CITRATE, 30% PEG 400)
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1add
20.1 MTris-HCl1reservoir
30.2 Msodium citrate1reservoir
430 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2002 / Details: BENT + TOROIDAL
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. obs: 12124 / % possible obs: 99.5 % / Redundancy: 9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 32
Reflection shellResolution: 1.94→2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 7.3 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 108633
Reflection shell
*PLUS
Lowest resolution: 2.01 Å / % possible obs: 99.3 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.94→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.981 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM BOTH THE N- AND C-TERMINII WERE NOT VISIBLE IN THE ELECTRON DENSITY. THESE RESIDUES WERE OMITTED FROM THE MODEL. THE REFINED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM BOTH THE N- AND C-TERMINII WERE NOT VISIBLE IN THE ELECTRON DENSITY. THESE RESIDUES WERE OMITTED FROM THE MODEL. THE REFINED MODEL CONTAINS RESIDUES 7- 73. RESIDUES 7-10 OF THE N-TERMINUS ARE NOT IN WELL DEFINED ELECTRON DENSITY. UNACCOUNTED SOLVENT DENSITY IS LOCATED CLOSE TO RESIDUES TYR18 AND TRP35
RfactorNum. reflection% reflectionSelection details
Rfree0.228 578 4.8 %RANDOM
Rwork0.2 ---
obs-11530 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 24.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20.63 Å20 Å2
2--1.27 Å20 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 1.94→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms568 0 28 99 695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021612
X-RAY DIFFRACTIONr_bond_other_d0.0020.02510
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.966830
X-RAY DIFFRACTIONr_angle_other_deg0.96431195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.054566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.283
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02642
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02126
X-RAY DIFFRACTIONr_nbd_refined0.2110.2128
X-RAY DIFFRACTIONr_nbd_other0.2460.2586
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.2359
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2670.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3710.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2861.5334
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2482542
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1873278
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9964.5288
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.208 52
Rwork0.228 819
Software
*PLUS
Name: REFMAC / Version: 5.1.24 24/04/2001 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199 / Rfactor Rfree: 0.2284 / Rfactor Rwork: 0.2003
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7

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