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- PDB-6i1q: Iodide structure of Trichoderma reesei Carbohydrate-Active Enzyme... -

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Basic information

Entry
Database: PDB / ID: 6i1q
TitleIodide structure of Trichoderma reesei Carbohydrate-Active Enzymes Family AA12
ComponentsSoluble quino protein glucose dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / carbohydrate-active enzymes / PQQ
Function / homologySoluble quinoprotein glucose/sorbosone dehydrogenase / Six-bladed beta-propeller, TolB-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / IODIDE ION / TRIETHYLENE GLYCOL / Soluble quino protein glucose dehydrogenase
Function and homology information
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsTurbe-Doan, A. / Record, E. / Lombard, V. / Kumar, R. / Henrissat, B. / Levasseur, A. / Garron, M.L.
CitationJournal: Appl.Environ.Microbiol. / Year: 2019
Title: The functional and structural characterization ofTrichoderma reeseidehydrogenase belonging to the PQQ dependent family of Carbohydrate-Active Enzymes Family AA12.
Authors: Turbe-Doan, A. / Record, E. / Lombard, V. / Kumar, R. / Levasseur, A. / Henrissat, B. / Garron, M.L.
History
DepositionOct 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble quino protein glucose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7139
Polymers42,6801
Non-polymers2,0338
Water2,414134
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint16 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.780, 82.780, 140.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Soluble quino protein glucose dehydrogenase


Mass: 42680.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30) (fungus)
Strain: ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30 / Gene: M419DRAFT_36756 / Production host: Aspergillus niger (mold) / References: UniProt: A0A024S820

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Sugars , 2 types, 5 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 137 molecules

#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: I
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 55-60% PEG550 MME, 0.1M HEPES. Crystals were brievely soaked in 1M KI solution
PH range: 8-5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.65312 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.65312 Å / Relative weight: 1
ReflectionResolution: 1.99→45 Å / Num. obs: 764115 / % possible obs: 99.5 % / Redundancy: 12 % / CC1/2: 0.99 / Rrim(I) all: 0.09 / Net I/σ(I): 20.44
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 1.07 % / Num. unique obs: 4361 / CC1/2: 0.89 / Rrim(I) all: 0.79 / % possible all: 93

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.99→45 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.433 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.143
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 1701 5 %RANDOM
Rwork0.1848 ---
obs0.1866 32304 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.01 Å2 / Biso mean: 33.534 Å2 / Biso min: 15.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.24 Å2
Refinement stepCycle: final / Resolution: 1.99→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 124 134 3238
Biso mean--65.7 36.49 -
Num. residues----399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0143180
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172687
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.7144368
X-RAY DIFFRACTIONr_angle_other_deg1.0761.696301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.095398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26623.397156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7715424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1551516
X-RAY DIFFRACTIONr_chiral_restr0.1370.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023621
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02578
LS refinement shellResolution: 1.993→2.045 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 116 -
Rwork0.271 2190 -
all-2306 -
obs--93.93 %

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