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- PDB-4a29: Structure of the engineered retro-aldolase RA95.0 -

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Basic information

Entry
Database: PDB / ID: 4a29
TitleStructure of the engineered retro-aldolase RA95.0
ComponentsENGINEERED RETRO-ALDOL ENZYME RA95.0
KeywordsDE NOVO PROTEIN / ENGINEERED ENZYME / RETRO-ALDOLASE / DIRECTED EVOLUTION
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
1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE / D-MALATE / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsGiger, L. / Caner, S. / Kast, P. / Baker, D. / Ban, N. / Hilvert, D.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Evolution of a designed retro-aldolase leads to complete active site remodeling.
Authors: Giger, L. / Caner, S. / Obexer, R. / Kast, P. / Baker, D. / Ban, N. / Hilvert, D.
History
DepositionSep 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jul 31, 2013Group: Database references
Revision 1.4May 15, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: ENGINEERED RETRO-ALDOL ENZYME RA95.0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0873
Polymers29,7101
Non-polymers3762
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.940, 62.590, 79.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ENGINEERED RETRO-ALDOL ENZYME RA95.0


Mass: 29710.219 Da / Num. of mol.: 1 / Fragment: TIM-BARREL FOLD, RESIDUES 1-258
Source method: isolated from a genetically manipulated source
Details: ARTIFICIAL GENE. THE SEQUENCE WAS COMPUTATIONALLY DESIGNED BASED ON INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE NATURALLY FOUND IN SULFOLOBUS SOLFATARICUS.
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: Q06121*PLUS, indole-3-glycerol-phosphate synthase
#2: Chemical ChemComp-3NK / 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE


Mass: 242.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14O3
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growTemperature: 301 K / Method: vapor diffusion
Details: 0.2 M DL-MALIC ACID PH 7.0, 20% W/V PEG 3350, 28 DEGREES CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 101040 / % possible obs: 91.8 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 34.14
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.21 / % possible all: 57.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LBL

1lbl


Resolution: 1.1→7.98 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 11.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.137 2030 2 %
Rwork0.12 --
obs0.12 100713 91.8 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 96.57 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9032 Å20 Å20 Å2
2---1.8522 Å20 Å2
3---0.949 Å2
Refinement stepCycle: LAST / Resolution: 1.1→7.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1991 0 26 369 2386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092404
X-RAY DIFFRACTIONf_angle_d1.2973288
X-RAY DIFFRACTIONf_dihedral_angle_d00
X-RAY DIFFRACTIONf_chiral_restr0.07370
X-RAY DIFFRACTIONf_plane_restr0.007438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.12740.1877750.15814340X-RAY DIFFRACTION57
1.1274-1.15780.15451300.13775226X-RAY DIFFRACTION69
1.1578-1.19180.15421280.12326404X-RAY DIFFRACTION84
1.1918-1.23010.13991500.12277261X-RAY DIFFRACTION95
1.2301-1.27390.13671470.11617369X-RAY DIFFRACTION97
1.2739-1.32470.13791530.1097389X-RAY DIFFRACTION97
1.3247-1.38470.12451480.09937471X-RAY DIFFRACTION97
1.3847-1.45730.11871550.09687428X-RAY DIFFRACTION97
1.4573-1.5480.11841550.09257468X-RAY DIFFRACTION98
1.548-1.66650.13161550.09127519X-RAY DIFFRACTION98
1.6665-1.83240.1221560.09747587X-RAY DIFFRACTION99
1.8324-2.09330.12821550.10487615X-RAY DIFFRACTION98
2.0933-2.62170.14831610.11547717X-RAY DIFFRACTION99
2.6217-7.98120.1411620.14627889X-RAY DIFFRACTION98

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