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- PDB-3b5l: Crystal Structure of a Novel Engineered Retroaldolase: RA-61 -

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Basic information

Entry
Database: PDB / ID: 3b5l
TitleCrystal Structure of a Novel Engineered Retroaldolase: RA-61
ComponentsEndoxylanase
KeywordsHYDROLASE / jelly roll / retroaldolase / engineered / alpha-beta / computationally designed / Glycosidase / Xylan degradation
Function / homology
Function and homology information


polysaccharide binding / endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process
Similarity search - Function
Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 ...Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / CBM2/CBM3, carbohydrate-binding domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
AMMONIUM ION / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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
DepositionOct 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Endoxylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1455
Polymers21,9171
Non-polymers2284
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.190, 66.060, 66.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endoxylanase


Mass: 21916.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others)
Description: Computationally designed based on the structure of thermophilic b-1,4-xylanase from Nonomuraea flexuosa
Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q8GMV7*PLUS, endo-1,4-beta-xylanase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.9536.96
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop6.51.9M Ammonium Sulfate, 0.1M MES pH 6.5, 5% v/v PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2982vapor diffusion, hanging drop6.52.0M Ammonium Sulfate, 0.1M MES pH 6.5, 5% v/v PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2983vapor diffusion, hanging drop6.52.1M Ammonium Sulfate, 0.1M MES pH 6.5, 5% v/v PEG400, 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: Oct 1, 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: 1.8→46.73 Å / Num. all: 16489 / Num. obs: 16082 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.059 / Χ2: 0.96 / Net I/σ(I): 12 / Scaling rejects: 424
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.45 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.1 / Num. measured all: 3300 / Num. unique all: 1347 / Χ2: 0.81 / % possible all: 83.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.8 Å33.71 Å
Translation1.8 Å33.71 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
CrystalCleardata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRUNCATED 1m4w

1m4w


Resolution: 1.8→33.71 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.799 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 819 5.1 %RANDOM
Rwork0.203 ---
obs0.206 16082 97.53 %-
all-16082 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.723 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2---0.12 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 12 174 1718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211591
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.8962172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3175197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42322.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.63415214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.772159
X-RAY DIFFRACTIONr_chiral_restr0.0710.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021246
X-RAY DIFFRACTIONr_nbd_refined0.1710.2691
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21047
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0790.223
X-RAY DIFFRACTIONr_mcbond_it0.3131.5993
X-RAY DIFFRACTIONr_mcangle_it0.53921553
X-RAY DIFFRACTIONr_scbond_it0.8353735
X-RAY DIFFRACTIONr_scangle_it1.1364.5619
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 68 -
Rwork0.318 904 -
all-972 -
obs--80.93 %
Refinement TLS params.Method: refined / Origin x: -5.8322 Å / Origin y: -10.112 Å / Origin z: 13.7669 Å
111213212223313233
T-0.0097 Å20.0051 Å20.0031 Å2--0.0266 Å20.002 Å2---0.0217 Å2
L0.2816 °2-0.1189 °2-0.2134 °2-0.4856 °20.2626 °2--0.7453 °2
S-0.0154 Å °0.0147 Å °-0.0001 Å °0.016 Å °-0.0038 Å °0.0089 Å °0.0057 Å °-0.0405 Å °0.0193 Å °

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