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- PDB-4pvi: Crystal structure of GH62 hydrolase in complex with xylotriose -

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Basic information

Entry
Database: PDB / ID: 4pvi
TitleCrystal structure of GH62 hydrolase in complex with xylotriose
ComponentsGH62 hydrolase
KeywordsHYDROLASE / Arabinofuranosidase / arabinofuranohydrolase / GH62 hydrolase / fungal genomics / arabinoxylan / lignocellulose degradation / xylotriose
Function / homology
Function and homology information


L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / xylan catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase, family 62, arabinosidase / Glycosyl hydrolase family 62 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
4beta-beta-xylotriose / PHOSPHATE ION / Alpha-L-arabinofuranosidase
Similarity search - Component
Biological speciesScytalidium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsNocek, B. / Kaur, A.P. / Xu, X. / Cui, H. / Savchenko, A.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of GH62 hydrolase in complex with xylotriose
Authors: Kaur, A.P. / Nocek, B. / Xu, X. / Lowden, M.J. / Leyva, J.F. / Stogios, P.J. / Cui, H. / Leo, R.D. / Powlowski, J. / Tsang, A. / Savchenko, A.
History
DepositionMar 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH62 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5684
Polymers38,9641
Non-polymers6043
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.445, 72.445, 62.099
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Detailsmonomer

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Components

#1: Protein GH62 hydrolase


Mass: 38964.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scytalidium thermophilum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059U759*PLUS
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 414.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylotriose
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.2M KH2PO4, 20% PEG3350, 2 mM CaCl2, 20 mM xylotriose , pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.48→23.713 Å / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 22
Reflection shellResolution: 1.48→1.51 Å / % possible all: 96.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
CCP4model building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PVA

4pva


Resolution: 1.48→23.713 Å / SU ML: 0.12 / σ(F): 1.61 / Phase error: 16.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1588 3444 5.04 %
Rwork0.1286 --
obs0.1302 68294 86.12 %
all-71738 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→23.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 0 38 515 3195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112819
X-RAY DIFFRACTIONf_angle_d1.5073876
X-RAY DIFFRACTIONf_dihedral_angle_d21.5011055
X-RAY DIFFRACTIONf_chiral_restr0.134409
X-RAY DIFFRACTIONf_plane_restr0.008503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4796-1.49990.2066880.19941289X-RAY DIFFRACTION28
1.4999-1.52130.2331110.19541820X-RAY DIFFRACTION39
1.5213-1.5440.2489960.19132199X-RAY DIFFRACTION47
1.544-1.56810.20531410.18442230X-RAY DIFFRACTION49
1.5681-1.59380.20321200.17052323X-RAY DIFFRACTION49
1.5938-1.62130.19611260.15992235X-RAY DIFFRACTION49
1.6213-1.65080.16151040.15522342X-RAY DIFFRACTION49
1.6508-1.68250.17431160.15382265X-RAY DIFFRACTION49
1.6825-1.71690.18631140.1522299X-RAY DIFFRACTION49
1.7169-1.75420.17321010.14812324X-RAY DIFFRACTION49
1.7542-1.7950.21321260.14342277X-RAY DIFFRACTION49
1.795-1.83980.18471190.13892282X-RAY DIFFRACTION49
1.8398-1.88960.14971220.13692244X-RAY DIFFRACTION49
1.8896-1.94510.17611460.13992367X-RAY DIFFRACTION51
1.9451-2.00790.15571320.1332412X-RAY DIFFRACTION53
2.0079-2.07960.15871260.13352683X-RAY DIFFRACTION57
2.0796-2.16280.1591450.12662724X-RAY DIFFRACTION59
2.1628-2.26120.16161470.12563042X-RAY DIFFRACTION65
2.2612-2.38030.1631570.12023285X-RAY DIFFRACTION71
2.3803-2.52930.14931850.12293370X-RAY DIFFRACTION73
2.5293-2.72430.16431870.12443485X-RAY DIFFRACTION74
2.7243-2.9980.15842080.12453376X-RAY DIFFRACTION74
2.998-3.43070.16741910.11653330X-RAY DIFFRACTION72
3.4307-4.3180.13971230.11093297X-RAY DIFFRACTION70
4.318-23.71620.12382130.12043350X-RAY DIFFRACTION73
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)
10.1837-0.1518-0.02080.35150.00270.260.00450.0208-0.0033-0.1349-0.004-0.1820.02060.05780.08250.10070.00910.03130.0774-0.00770.108816.4337-24.0659-5.7023
20.2128-0.09440.01110.33060.07550.13020.0392-0.02710.0765-0.06110.001-0.0713-0.05380.00740.01530.1168-0.00620.00770.0782-0.00090.10137.0476-9.5938-0.609
30.09710.017-0.05830.35150.14740.07150.0233-0.01370.0157-0.03140.00850.07670.019-0.02940.01680.08710.0005-0.00890.08170.00660.0679-3.5869-16.4895.0341
40.0820.041-0.11640.1696-0.00480.103-0.0501-0.0105-0.09220.01030.05420.01720.0457-0.0012-0.0050.10590.0003-0.01450.08570.01110.0922-0.1168-30.27155.3913
50.03440.06630.01690.047-0.00060.0138-0.0447-0.08260.00220.02440.08940.07970.0233-0.031300.1116-0.00050.00270.09370.01320.1094-4.0917-31.01186.9807
60.0150.01210.00650.0169-0.00640.017-0.02060.0742-0.0115-0.06690.125-0.17980.110.094100.12490.02490.00770.1175-0.01840.14615.9203-38.34323.1858
70.01860.0134-0.03810.0031-0.02980.0320.00170.0450.0349-0.12780.0049-0.01310.02680.03150.00310.1580.0068-0.00350.0890.00050.08011.4817-26.3637-8.4198
80.05070.0413-0.08050.0863-0.06850.07260.0677-0.0561-0.12380.0294-0.055-0.19540.05370.023700.11130.0089-0.01310.11440.00790.142918.1914-28.95113.875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -7 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 207 )
4X-RAY DIFFRACTION4chain 'A' and (resid 208 through 237 )
5X-RAY DIFFRACTION5chain 'A' and (resid 238 through 257 )
6X-RAY DIFFRACTION6chain 'A' and (resid 258 through 273 )
7X-RAY DIFFRACTION7chain 'A' and (resid 274 through 294 )
8X-RAY DIFFRACTION8chain 'A' and (resid 295 through 321 )

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