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- PDB-4ou1: Crystal structure of a computationally designed retro-aldolase co... -

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Basic information

Entry
Database: PDB / ID: 4ou1
TitleCrystal structure of a computationally designed retro-aldolase covalently bound to folding probe 1 [(6-methoxynaphthalen-2-yl)(oxiran-2-yl)methanol]
ComponentsRetro-aldolase, design RA114
KeywordsLYASE / TIM barrel / retro-aldolase
Function / homology
Function and homology information


indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process
Similarity search - Function
Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-2V7 / BENZOIC ACID / PHOSPHATE ION / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBhabha, G. / Zhang, X. / Ekiert, D.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts.
Authors: Liu, Y. / Tan, Y.L. / Zhang, X. / Bhabha, G. / Ekiert, D.C. / Genereux, J.C. / Cho, Y. / Kipnis, Y. / Bjelic, S. / Baker, D. / Kelly, J.W.
History
DepositionFeb 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Apr 23, 2014Group: Database references
Revision 1.3Sep 20, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Retro-aldolase, design RA114
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3425
Polymers29,7971
Non-polymers5444
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.730, 61.730, 121.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Retro-aldolase, design RA114


Mass: 29797.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: pET29-b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: Q06121*PLUS, Lyases; Carbon-carbon lyases
#2: Chemical ChemComp-2V7 / (1S,2S)-1-(6-methoxynaphthalen-2-yl)propane-1,2-diol / (6-methoxynaphthalen-2-yl)(oxiran-2-yl)methanol, bound form


Mass: 232.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16O3
#3: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRESIDUE A LYS 210 WAS MODIFIED WITH (6-METHOXYNAPHTHALEN-2-YL)(OXIRAN-2-YL)METHANOL.

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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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M phosphate/citrate, pH 4.2, 1.6 M sodium phosphate monobasic, 0.4 M potassium phosphate dibasic, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2013
RadiationMonochromator: Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 74719 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 14.7 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 6.3 % / Rmerge(I) obs: 2.37 / Mean I/σ(I) obs: 0.93 / % possible all: 98.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_1593)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TC7

3tc7


Resolution: 1.25→40.179 Å / SU ML: 0.13 / σ(F): 1.33 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 2489 3.34 %RANDOM
Rwork0.1748 ---
obs0.1758 74632 99.36 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.1 Å2
Refinement stepCycle: LAST / Resolution: 1.25→40.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 36 223 2259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012230
X-RAY DIFFRACTIONf_angle_d1.4033031
X-RAY DIFFRACTIONf_dihedral_angle_d13.185882
X-RAY DIFFRACTIONf_chiral_restr0.08338
X-RAY DIFFRACTIONf_plane_restr0.007393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.2740.32141260.30653953X-RAY DIFFRACTION98
1.274-1.30.44891200.40943878X-RAY DIFFRACTION98
1.3-1.32830.39211440.33943901X-RAY DIFFRACTION98
1.3283-1.35920.27781440.22243971X-RAY DIFFRACTION100
1.3592-1.39320.22891390.19663994X-RAY DIFFRACTION100
1.3932-1.43080.21581380.20533973X-RAY DIFFRACTION99
1.4308-1.4730.31461380.26843976X-RAY DIFFRACTION99
1.473-1.52050.28311330.20343951X-RAY DIFFRACTION99
1.5205-1.57480.21051380.1563995X-RAY DIFFRACTION100
1.5748-1.63790.21521380.14873994X-RAY DIFFRACTION100
1.6379-1.71240.19051430.14974026X-RAY DIFFRACTION100
1.7124-1.80270.18171410.15124013X-RAY DIFFRACTION100
1.8027-1.91570.23321370.18844010X-RAY DIFFRACTION100
1.9157-2.06360.24881380.19563980X-RAY DIFFRACTION98
2.0636-2.27120.23891360.19084037X-RAY DIFFRACTION100
2.2712-2.59980.17491420.14784073X-RAY DIFFRACTION100
2.5998-3.27530.16881480.16344129X-RAY DIFFRACTION100
3.2753-40.19980.17321460.1584289X-RAY DIFFRACTION99

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