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- PDB-3zxj: Engineering the active site of a GH43 glycoside hydrolase generat... -

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Basic information

Entry
Database: PDB / ID: 3zxj
TitleEngineering the active site of a GH43 glycoside hydrolase generates a biotechnologically significant enzyme that displays both endo- xylanase and exo-arabinofuranosidase activity
ComponentsHIAXHD3
KeywordsHYDROLASE / ARABINOSIDASE / XYLOSIDASE
Function / homologyGlycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Jelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHUMICOLA INSOLENS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsMcKee, L.S. / Pena, M.J. / Rogowski, A. / Jackson, A. / Lewis, R.J. / York, W.S. / Krogh, K.B.R.M. / Vikso-Nielsen, A. / Skjot, M. / Gilbert, H.J. / Marles-Wright, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Introducing Endo-Xylanase Activity Into an Exo-Acting Arabinofuranosidase that Targets Side Chains.
Authors: Mckee, L.S. / Pena, M.J. / Rogowski, A. / Jackson, A. / Lewis, R.J. / York, W.S. / Krogh, K.B.R.M. / Vikso-Nielsen, A. / Skjot, M. / Gilbert, H.J. / Marles-Wright, J.
History
DepositionAug 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Other
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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: HIAXHD3
B: HIAXHD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,04210
Polymers122,0072
Non-polymers1,0358
Water15,259847
1
A: HIAXHD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6276
Polymers61,0031
Non-polymers6245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HIAXHD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4154
Polymers61,0031
Non-polymers4113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.318, 78.260, 95.767
Angle α, β, γ (deg.)90.00, 103.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HIAXHD3


Mass: 61003.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMICOLA INSOLENS (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: non-reducing end alpha-L-arabinofuranosidase
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsGENBANK CAL81199

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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: 2.06 Å3/Da / Density % sol: 40.3 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M BIS-TRIS PH 6.5, 22 % (W/V) PEG3350, 2 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 4, 2008
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→47.75 Å / Num. obs: 80563 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.2 % / Biso Wilson estimate: 16.09 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.8
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.85→47.75 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.214 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.18923 4029 5 %RANDOM
Rwork0.15461 ---
obs0.15638 76186 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.738 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.05 Å2
2---0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8356 0 66 847 9269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.028719
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.93711892
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80851075
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.57922.282425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.457151197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0691586
X-RAY DIFFRACTIONr_chiral_restr0.0960.21242
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216896
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 274 -
Rwork0.185 5488 -
obs--100 %
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)
10.8772-0.012-0.50080.15510.06250.5564-0.03430.0265-0.0235-0.0072-0.0450.04670.0482-0.05630.07930.0771-0.0055-0.00880.0164-0.01310.0875-9.3702-5.1914-12.0774
20.6041-0.192-0.52310.3977-0.02141.58790.02080.079-0.01370.0235-0.0458-0.037-0.1568-0.23870.0250.03830.0203-0.02030.054-0.01750.0661-22.42573.5889-9.5244
31.0924-0.4217-0.58440.22630.24671.3519-0.1471-0.0477-0.14670.0851-0.03130.04070.2012-0.14610.17840.0747-0.03270.03560.0591-0.00060.0979-19.0171-11.08351.3095
40.61960.0004-0.4131.49730.14641.1471-0.03370.126-0.0619-0.131-0.01270.07620.0828-0.07810.04630.04860.0019-0.01460.03190.00070.07681.8087-7.709-25.106
50.8462-0.0947-0.29560.26880.0410.8093-0.0716-0.0847-0.00860.01660.04730.01430.02320.16040.02430.05320.01250.00010.03830.00830.05113.672-6.7724-12.9247
61.4502-0.0367-0.9860.32540.38881.0956-0.12710.0605-0.07050.0398-0.05680.10210.131-0.08170.18390.08420.00020.0030.02980.00510.0973-15.2732-41.7365-38.0305
70.8049-0.2061-0.55190.45430.37371.7088-0.02770.1462-0.02310.0109-0.18790.0208-0.1206-0.30050.21550.02850.0141-0.03210.1009-0.04680.0813-28.4428-33.2163-36.1569
81.3724-0.2608-1.03050.12570.5032.2586-0.40310.0247-0.26840.1321-0.06890.10270.501-0.16050.4720.1657-0.04790.12610.0386-0.02070.1531-25.5114-46.9617-24.1062
90.77170.091-0.38551.64340.6240.9136-0.04760.1244-0.0579-0.07560.00860.0980.0097-0.09020.0390.0471-0.0034-0.02020.04920.00380.0582-4.0901-45.9859-50.4419
101.4388-0.4789-0.57960.39730.28731.1104-0.1307-0.17970.00990.03480.17570.01590.05460.2424-0.04490.05090.0188-0.01280.0973-0.00310.03327.7312-43.8215-38.5021
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 108
2X-RAY DIFFRACTION2A109 - 242
3X-RAY DIFFRACTION3A243 - 341
4X-RAY DIFFRACTION4A342 - 376
5X-RAY DIFFRACTION5A378 - 559
6X-RAY DIFFRACTION6B30 - 108
7X-RAY DIFFRACTION7B109 - 242
8X-RAY DIFFRACTION8B243 - 341
9X-RAY DIFFRACTION9B342 - 376
10X-RAY DIFFRACTION10B377 - 558

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