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- PDB-5an7: Structure of the engineered retro-aldolase RA95.5-8F with a bound... -

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Basic information

Entry
Database: PDB / ID: 5an7
TitleStructure of the engineered retro-aldolase RA95.5-8F with a bound 1,3-diketone inhibitor
ComponentsRA95.5-8F
KeywordsLYASE / RETRO-ALDOLASE / PROTEIN ENGINEERING / ENZYME DESIGN / 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, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / 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
(2E)-1-(6-methoxynaphthalen-2-yl)but-2-en-1-one / PHOSPHATE ION / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsObexer, R. / Mittl, P.R.E. / Hilvert, D.
CitationJournal: Nat Chem / Year: 2017
Title: Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase.
Authors: Obexer, R. / Godina, A. / Garrabou, X. / Mittl, P.R. / Baker, D. / Griffiths, A.D. / Hilvert, D.
History
DepositionSep 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RA95.5-8F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3534
Polymers29,9361
Non-polymers4163
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.110, 84.430, 37.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2112-

HOH

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Components

#1: Protein RA95.5-8F


Mass: 29936.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE SEQUENCE WAS DESIGNED BASED ON INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE NATURALLY FOUND IN SULFOLOBUS SOLFATARICUS
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q06121*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-LLK / (2E)-1-(6-methoxynaphthalen-2-yl)but-2-en-1-one


Mass: 226.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE (CC1): COVALENTLY BONDED TO LYSINE 2083

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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: 1.99 Å3/Da / Density % sol: 38.29 % / Description: NONE
Crystal growTemperature: 293 K / pH: 4.5
Details: 0.1M HEPES, 0.8M SODIUM PHOSPHATE, 0.8M POTASSIUM PHOSPHATE, PH 4.5, 20 DEGREES CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.1→37.64 Å / Num. obs: 167220 / % possible obs: 89.2 % / Observed criterion σ(I): 0 / Redundancy: 3.07 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.65
Reflection shellResolution: 1.1→1.17 Å / Mean I/σ(I) obs: 0.89 / % possible all: 44.3

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Processing

Software
NameClassification
SHELXLrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A2R

4a2r


Resolution: 1.1→37.6 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1877 3877 -RANDOM
obs0.1362 -89.2 %-
all-76639 --
Refinement stepCycle: LAST / Resolution: 1.1→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 27 284 2294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d2.377
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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