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- PDB-3hoj: Crystal Structure of a Novel Engineered Retroaldolase: RA-22 -

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Basic information

Entry
Database: PDB / ID: 3hoj
TitleCrystal Structure of a Novel Engineered Retroaldolase: RA-22
ComponentsRETROALDOLASE-22
KeywordsLYASE / TIM BARREL / RETROALDOLASE / ENGINEERED COMPUTATIONALLY DESIGNED
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsStoddard, B.L. / Doyle, L.A.
CitationJournal: Science / Year: 2008
Title: De Novo Computational Design of Retro-Aldol Enzymes
Authors: Jiang, L. / Althoff, E.A. / Clemente, F.R. / Doyle, L. / Rothlisberger, D. / Zanghellini, A. / Gallaher, J.L. / Betker, J.L. / Tanaka, F. / Barbas, C.F. / Hilvert, D. / Houk, K.N. / Stoddard, B.L. / Baker, D.
History
DepositionJun 2, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionAug 25, 2009ID: 3B5V
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RETROALDOLASE-22


Theoretical massNumber of molelcules
Total (without water)28,4571
Polymers28,4571
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.047, 73.583, 47.399
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein RETROALDOLASE-22


Mass: 28456.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others)
Description: THE SEQUENCE WAS COMPUTATIONALLY DESIGNED BASED ON INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE NATURALLY FOUND IN SULFOLOBUS SOLFATARICUS.
Plasmid: PET29B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: indole-3-glycerol-phosphate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.6, 27% PEG4000 FOLLOWED BY FURTHER EQUILIBRATION AFTER INITIAL CRYSTALLIZATION OVER 0.2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.6, 30% ...Details: 0.2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.6, 27% PEG4000 FOLLOWED BY FURTHER EQUILIBRATION AFTER INITIAL CRYSTALLIZATION OVER 0.2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.6, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 24, 2007 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→36.02 Å / Num. obs: 13187 / % possible obs: 98.9 % / Redundancy: 3.48 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.068 / Χ2: 0.97 / Net I/σ(I): 10.4 / Scaling rejects: 348
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3.8 / Num. measured all: 3735 / Num. unique all: 1282 / Χ2: 1.15 / % possible all: 97.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å36.02 Å
Translation2.2 Å36.02 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→36.01 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.267 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.753 / SU B: 7.971 / SU ML: 0.205 / SU R Cruickshank DPI: 0.369 / SU Rfree: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.293 648 4.9 %RANDOM
Rwork0.236 ---
obs0.238 13184 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.68 Å2 / Biso mean: 25.724 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 0 145 2070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221956
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9762648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5685246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08423.61483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.20915349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6831516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021445
X-RAY DIFFRACTIONr_nbd_refined0.1880.2885
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21338
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2124
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.29
X-RAY DIFFRACTIONr_mcbond_it0.491.51275
X-RAY DIFFRACTIONr_mcangle_it0.82921986
X-RAY DIFFRACTIONr_scbond_it1.3853776
X-RAY DIFFRACTIONr_scangle_it2.2764.5662
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 59 -
Rwork0.259 898 -
all-957 -
obs--96.86 %

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