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- PDB-3tdn: Computationally designed two-fold symmetric Tim-barrel protein, FLR -

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Basic information

Entry
Database: PDB / ID: 3tdn
TitleComputationally designed two-fold symmetric Tim-barrel protein, FLR
ComponentsFLR SYMMETRIC ALPHA-BETA TIM BARREL
KeywordsDE NOVO PROTEIN / SYMMETRIC SUPERFOLD / TIM-BARREL
Function / homologyRossmann fold - #12600 / Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHarp, J.M. / Fortenberry, C. / Bowman, E. / Profitt, W. / Dorr, B. / Mizoue, L. / Meiler, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Exploring symmetry as an avenue to the computational design of large protein domains.
Authors: Fortenberry, C. / Bowman, E.A. / Proffitt, W. / Dorr, B. / Combs, S. / Harp, J. / Mizoue, L. / Meiler, J.
History
DepositionAug 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Apr 3, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FLR SYMMETRIC ALPHA-BETA TIM BARREL
B: FLR SYMMETRIC ALPHA-BETA TIM BARREL


Theoretical massNumber of molelcules
Total (without water)53,3952
Polymers53,3952
Non-polymers00
Water4,666259
1
A: FLR SYMMETRIC ALPHA-BETA TIM BARREL

A: FLR SYMMETRIC ALPHA-BETA TIM BARREL


Theoretical massNumber of molelcules
Total (without water)53,3952
Polymers53,3952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
MethodPISA
2
B: FLR SYMMETRIC ALPHA-BETA TIM BARREL


Theoretical massNumber of molelcules
Total (without water)26,6971
Polymers26,6971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.222, 67.222, 124.658
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein FLR SYMMETRIC ALPHA-BETA TIM BARREL


Mass: 26697.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: ESCHERICHIA COLI (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS COMPUTATIONALLY DESIGNED BASED ON A TIM-BARREL. THE FULL CRYSTALLIZED SEQUENCE HAS ...THE SEQUENCE IS COMPUTATIONALLY DESIGNED BASED ON A TIM-BARREL. THE FULL CRYSTALLIZED SEQUENCE HAS BEEN PROVIDED IN SEQRES REMARK. HOWEVER, CHAIN A IS ON A CRYSTALLOGRAPHIC AXIS AND THE FULL MOLECULE IS GENERATE BY SYMMETRY AS DESCRIBED IN REMARK 350 AND THEREFORE RESIDUES 122-242 ARE ABSENT FROM THE FINAL MODEL.

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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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.2
Details: 20% PEG 1000, 0.1M SODIUM CITRATE, 0.1 M AMMONIUM CHLORIDE, pH 4.2, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.072
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2009
RadiationMonochromator: KOHZU DUAL DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 63971 / % possible obs: 98 % / Redundancy: 9.7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 19.35
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 3.01 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: COMPUTATIONAL MODEL

Resolution: 1.4→42.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.793 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3264 5.1 %RANDOM
Rwork0.157 ---
obs0.159 60459 97.9 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 21.27 Å2
Baniso -1Baniso -2Baniso -3
1--4.31 Å2-0 Å2-0 Å2
2---4.31 Å20 Å2
3---8.61 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 0 259 2978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222776
X-RAY DIFFRACTIONr_bond_other_d0.0010.021893
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9633750
X-RAY DIFFRACTIONr_angle_other_deg1.09634614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4635358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02123.451113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62915494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9031522
X-RAY DIFFRACTIONr_chiral_restr0.1460.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
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_it2.9161.51762
X-RAY DIFFRACTIONr_mcbond_other0.9811.5740
X-RAY DIFFRACTIONr_mcangle_it4.31122840
X-RAY DIFFRACTIONr_scbond_it5.27331014
X-RAY DIFFRACTIONr_scangle_it7.3324.5908
X-RAY DIFFRACTIONr_rigid_bond_restr2.35334669
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 236 -
Rwork0.175 4273 -
obs--95.05 %

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