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Basic information

Entry
Database: PDB / ID: 3nxf
TitleRobust computational design, optimization, and structural characterization of retroaldol enzymes
ComponentsRetro-Aldolase
KeywordsLYASE / computationally designed / retroaldolase / tim barrel
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAlthoff, E.A. / Jiang, L. / Wang, L. / Lassila, J.K. / Moody, J. / Bolduc, J. / Wang, Z.Z. / Smith, M. / Hari, S. / Herschlag, D. ...Althoff, E.A. / Jiang, L. / Wang, L. / Lassila, J.K. / Moody, J. / Bolduc, J. / Wang, Z.Z. / Smith, M. / Hari, S. / Herschlag, D. / Stoddard, B.L. / Baker, D.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.
Authors: Wang, L. / Althoff, E.A. / Bolduc, J. / Jiang, L. / Moody, J. / Lassila, J.K. / Giger, L. / Hilvert, D. / Stoddard, B. / Baker, D.
History
DepositionJul 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Nov 30, 2011Group: Database references
Revision 1.4Feb 1, 2012Group: Database references
Revision 1.5Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.6Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

Deposited unit
A: Retro-Aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9312
Polymers29,8351
Non-polymers961
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.916, 61.916, 121.241
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


Mass: 29835.410 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)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein at 5mg/ml in 100mm NaCl, 25mm Tris pH 7.5. Crystals grew at and near 2M ammonium sulfate, 4% PEG400, 100mm Na acetate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 31, 2009 / Details: Varimax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.09→53.61 Å / Num. all: 11053 / Num. obs: 10320 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 46.1 Å2 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.09-2.163.12.0716150.7199.9
2.4-2.493.95.9210870.29199.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A53, with design and adjacent residues pared to alanine

1a53


Resolution: 2.4→53.61 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.814 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.58 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26821 522 4.8 %RANDOM
Rwork0.22454 ---
all0.22672 11023 --
obs0.22672 10320 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.845 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20.7 Å20 Å2
2--1.4 Å20 Å2
3----2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→53.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 5 60 2065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222080
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9982817
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5275257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52323.54893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17215397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2891521
X-RAY DIFFRACTIONr_chiral_restr0.0910.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021516
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2975
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21419
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.01121303
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79732049
X-RAY DIFFRACTIONr_scbond_it2.3264889
X-RAY DIFFRACTIONr_scangle_it3.6356764
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 36 -
Rwork0.316 743 -
obs-743 98.23 %

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