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- PDB-2f2h: Structure of the YicI thiosugar Michaelis complex -

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Basic information

Entry
Database: PDB / ID: 2f2h
TitleStructure of the YicI thiosugar Michaelis complex
ComponentsPutative family 31 glucosidase yicI
KeywordsHYDROLASE / beta8alpha8 barrel
Function / homology
Function and homology information


xyloglucan 1,6-alpha-xylosidase activity / alpha-D-xyloside xylohydrolase / alpha-D-xyloside xylohydrolase / carbohydrate binding / carbohydrate metabolic process / identical protein binding
Similarity search - Function
glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-XTG / Alpha-xylosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKim, Y.-W. / Lovering, A.L. / Strynadka, N.C.J. / Withers, S.G.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Expanding the Thioglycoligase Strategy to the Synthesis of alpha-linked Thioglycosides Allows Structural Investigation of the Parent Enzyme/Substrate Complex
Authors: Kim, Y.-W. / Lovering, A.L. / Chen, H. / Kantner, T. / McIntosh, L.P. / Strynadka, N.C.J. / Withers, S.G.
History
DepositionNov 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Putative family 31 glucosidase yicI
B: Putative family 31 glucosidase yicI
C: Putative family 31 glucosidase yicI
D: Putative family 31 glucosidase yicI
E: Putative family 31 glucosidase yicI
F: Putative family 31 glucosidase yicI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)536,21441
Polymers529,8686
Non-polymers6,34635
Water36,0842003
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34770 Å2
ΔGint-197 kcal/mol
Surface area144320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.317, 175.841, 210.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Putative family 31 glucosidase yicI


Mass: 88311.281 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yicI / Plasmid: pET29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P31434

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Non-polymers , 5 types, 2038 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-XTG / 4-NITROPHENYL 6-THIO-6-S-ALPHA-D-XYLOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / 4-NITROPHENYL-(6-S-ALPHA-D-XYLOPYRANOSYL)-BETA-D-GLUCOPYRANOSIDE


Mass: 449.430 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C17H23NO11S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2003 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mg/ml protein, 100mM Na Acetate, pH 6.5, 2M Ammonium Sulphate , VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.95516 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95516 Å / Relative weight: 1
ReflectionResolution: 1.95→28.64 Å / Num. all: 375658 / Num. obs: 375731 / % possible obs: 86.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 7.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1.7 / Num. unique all: 55875 / Rsym value: 0.433 / % possible all: 88.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XSI

1xsi


Resolution: 1.95→28.64 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.39 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.168 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 18828 5 %RANDOM
Rwork0.18 ---
all0.182 375658 --
obs0.182 375658 86.36 %-
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: 18.288 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---1.31 Å20 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37392 0 404 2003 39799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02238885
X-RAY DIFFRACTIONr_bond_other_d0.0020.0233535
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.93952849
X-RAY DIFFRACTIONr_angle_other_deg0.963377786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.56554632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15723.8551992
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.421156060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.02415246
X-RAY DIFFRACTIONr_chiral_restr0.1250.25448
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0243686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028478
X-RAY DIFFRACTIONr_nbd_refined0.2050.27205
X-RAY DIFFRACTIONr_nbd_other0.1990.234318
X-RAY DIFFRACTIONr_nbtor_refined0.1850.218275
X-RAY DIFFRACTIONr_nbtor_other0.0910.221350
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.22120
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.224
X-RAY DIFFRACTIONr_mcbond_it1.1171.529375
X-RAY DIFFRACTIONr_mcbond_other0.2231.59450
X-RAY DIFFRACTIONr_mcangle_it1.33237062
X-RAY DIFFRACTIONr_scbond_it2.163319197
X-RAY DIFFRACTIONr_scangle_it3.0684.515787
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 1318 -
Rwork0.254 24949 -
obs-26267 82.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0261-0.0033-0.00180.06230.010.0292-0.0016-0.0047-0.00680.0080.0066-0.01360.00030.0014-0.005-0.00450.0044-0.00750.00610.0012-0.015166.433267.4999136.7472
20.05550.0116-0.00830.01090.00470.03570.0087-0.01030.00340.0115-0.00920.00410.0025-0.00560.0006-0.0054-0.00330.00810.0117-0.0027-0.017197.051187.6123148.9534
30.05010.0155-0.00160.0552-0.00040.0203-0.00410.0016-0.0054-0.00430.0020.0176-0.0009-0.00190.002-0.0106-0.0025-0.01160.0015-0.0014-0.004294.737674.9327109.4255
40.06860.0115-0.00550.0625-0.01170.0191-0.00490.0073-0.0071-0.01920.0046-0.01310.0009-0.00470.00020-0.00210.00320.0036-0.0057-0.0187166.82276.326896.1686
50.06710.0141-0.0010.08920.00910.0035-0.0070.0130.0204-0.01730.00770.01160.00230.0031-0.0007-0.00070.0009-0.0124-0.00310.005-0.0102129.1174138.9929101.1689
60.03950.01970.00730.047-0.00470.02680.0017-0.00660.0110.0081-0.00010.0087-0.0050.0023-0.00170.00070.00040.00040.0002-0.0107-0.0135148.6637138.7837137.6325
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 773 / Label seq-ID: 1 - 773

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD
55EE
66FF

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