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

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Basic information

Entry
Database: PDB / ID: 3zxk
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 / SUGAR BINDING PROTEIN
Function / homologyGlycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Jelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesHUMICOLA INSOLENS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)122,6446
Polymers121,0752
Non-polymers1,5704
Water18,3031016
1
A: HIAXHD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3223
Polymers60,5371
Non-polymers7852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HIAXHD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3223
Polymers60,5371
Non-polymers7852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.380, 52.970, 146.870
Angle α, β, γ (deg.)90.00, 101.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HIAXHD3


Mass: 60537.340 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: Polysaccharide alpha-L-arabinofuranose-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-2[DXylpb1-4]DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a212h-1b_1-5][a211h-1a_1-4]/1-1-2-1/a4-b1_b2-c1_b4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-L-Araf]{}[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1016 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsGENBANK SEQUENCE REF CAL81199. D43A MUTATION.

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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: 7.5 / Details: 0.1 M HEPES PH 7.5 22.5 % (W/V) PEG4000 0.1 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Type: APS / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: May 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→33.68 Å / Num. obs: 177611 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 8.08 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.2
Reflection shellResolution: 1.44→1.47 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 9.8 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZXJ

3zxj


Resolution: 1.44→33.68 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.897 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20725 8835 5 %RANDOM
Rwork0.16649 ---
obs0.16853 167521 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.592 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.44→33.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8338 0 104 1016 9458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028753
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.93811954
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88851079
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.7422.22419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.424151245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2731585
X-RAY DIFFRACTIONr_chiral_restr0.180.21268
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216887
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_restr2.33738753
X-RAY DIFFRACTIONr_sphericity_free30.3335297
X-RAY DIFFRACTIONr_sphericity_bonded8.03459207
LS refinement shellResolution: 1.437→1.474 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 624 -
Rwork0.243 11554 -
obs--93.76 %
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)
10.47230.0208-0.13480.03010.00810.29020.012-0.0085-0.0090.0139-0.004300.00550.006-0.00770.0131-0.0018-0.00080.0009-0.00160.014613.139-11.708317.0563
20.2487-0.0899-0.08970.38870.17040.55540.01660.00520.0111-0.0282-0.01980.0045-0.0384-0.03120.00320.00810.00150.00060.0023-0.00060.01450.1018-3.650113.284
30.1748-0.0998-0.07830.14560.09340.2153-0.0042-0.0424-0.00040.02450.00340.0225-0.0052-0.00180.00090.0179-0.00560.0020.0172-0.00030.01933.2095-7.256931.0468
40.4059-0.0282-0.08330.9345-0.34520.8915-0.00660.0196-0.0415-0.03370.0140.02250.097-0.0441-0.00740.0108-0.0039-0.00260.0056-0.00690.016124.5414-22.50599.1536
50.275-0.0325-0.0620.15910.10550.3166-0.0019-0.0219-0.00260.00830.0031-0.01920.00670.0269-0.00120.0112-0.0007-0.00050.0056-0.00090.015136.2067-13.537617.4522
60.4883-0.1130.09430.11470.05810.13280.004-0.00620.01450.0039-0.0063-0.01590.0093-0.00270.00220.0174-0.00260.00150.01080.00020.014237.6767-32.252455.5432
70.428-0.0145-0.08540.26380.10.5318-0.00280.02660.028-0.01380.0075-0.0151-0.02040.0243-0.00460.0057-0.0037-0.00220.00450.00260.015750.7267-28.145947.8919
80.5001-0.0182-0.03560.11240.06030.1723-0.0160.001-0.06520.00830.0136-0.00750.03840.01930.00240.02270.0028-0.00360.0065-0.00220.021847.5508-46.227450.4238
90.0806-0.0324-0.06350.6259-0.0050.8112-0.0017-0.05240.02340.06240.0069-0.0272-0.00090.0178-0.00520.008-0.0003-0.00260.0358-0.01190.024726.3798-25.226966.9069
100.2326-0.0439-0.03430.25430.05480.1575-0.0050.0062-0.00140.00710.00070.01440.0063-0.02040.00430.0111-0.0021-0.00250.0147-0.00060.015614.5895-32.730957.5231
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 DIFFRACTION5A377 - 557
6X-RAY DIFFRACTION6B29 - 108
7X-RAY DIFFRACTION7B109 - 242
8X-RAY DIFFRACTION8B243 - 341
9X-RAY DIFFRACTION9B342 - 376
10X-RAY DIFFRACTION10B377 - 557

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