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- PDB-6f1j: Structure of a Talaromyces pinophilus GH62 Arabinofuranosidase in... -

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Basic information

Entry
Database: PDB / ID: 6f1j
TitleStructure of a Talaromyces pinophilus GH62 Arabinofuranosidase in complex with AraDNJ at 1.25A resolution
Componentsprotein
KeywordsHYDROLASE / biofuels / glycosidase / enzyme / enzyme inhibitor / sugar binding protein
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 / metal ion binding
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
1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL / DI(HYDROXYETHYL)ETHER / Alpha-L-arabinofuranosidase
Similarity search - Component
Biological speciesTalaromyces pinophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsMoroz, O.V. / Sobala, L. / Blagova, E. / Coyle, T. / Morkeberg Krogh, K.B.R. / Wei, P. / Stubbs, K. / Wilson, K.S. / Davies, G.J.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Structure of a Talaromyces pinophilus GH62 arabinofuranosidase in complex with AraDNJ at 1.25 angstrom resolution.
Authors: Moroz, O.V. / Sobala, L.F. / Blagova, E. / Coyle, T. / Peng, W. / Morkeberg Krogh, K.B.R. / Stubbs, K.A. / Wilson, K.S. / Davies, G.J.
History
DepositionNov 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein
B: protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,16812
Polymers69,2662
Non-polymers90210
Water11,854658
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-78 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.827, 88.978, 72.663
Angle α, β, γ (deg.)90.00, 95.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 25 - 324 / Label seq-ID: 25 - 324

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein protein


Mass: 34633.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: propeptide at the start / Source: (gene. exp.) Talaromyces pinophilus (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: A0A2H5BN17*PLUS

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Non-polymers , 5 types, 668 molecules

#2: Chemical ChemComp-EDG / 1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL


Mass: 133.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG2K MME, 0.2M KBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.93 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.25→33.52 Å / Num. obs: 149344 / % possible obs: 98 % / Redundancy: 3.1 % / Rpim(I) all: 0.04 / Net I/σ(I): 13.1
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 2.1 % / Num. unique obs: 6813 / Rpim(I) all: 0.28 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimlessdata scaling
MOLREPphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3wmy

3wmy


Resolution: 1.25→33.52 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.112 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.034 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13588 7516 5 %RANDOM
Rwork0.11972 ---
obs0.12055 141792 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 7.871 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20.13 Å2
2---0.04 Å20 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.25→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 50 658 5248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024890
X-RAY DIFFRACTIONr_bond_other_d0.0020.024126
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9336708
X-RAY DIFFRACTIONr_angle_other_deg0.9752.9939646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7715656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.50124.195205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.1615677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4951517
X-RAY DIFFRACTIONr_chiral_restr0.1040.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021063
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_it0.7710.6732507
X-RAY DIFFRACTIONr_mcbond_other0.770.6722506
X-RAY DIFFRACTIONr_mcangle_it1.0221.023160
X-RAY DIFFRACTIONr_mcangle_other1.0221.023161
X-RAY DIFFRACTIONr_scbond_it0.910.7662383
X-RAY DIFFRACTIONr_scbond_other0.9080.7662383
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1011.1043535
X-RAY DIFFRACTIONr_long_range_B_refined2.1578.4495142
X-RAY DIFFRACTIONr_long_range_B_other1.5828.0765063
X-RAY DIFFRACTIONr_rigid_bond_restr1.32139016
X-RAY DIFFRACTIONr_sphericity_free20.6685526
X-RAY DIFFRACTIONr_sphericity_bonded5.29159000
Refine LS restraints NCS

Ens-ID: 1 / Number: 19198 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 508 -
Rwork0.188 9649 -
obs--90.63 %

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