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- PDB-6ze4: FAD-dependent oxidoreductase from Chaetomium thermophilum in comp... -

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Basic information

Entry
Database: PDB / ID: 6ze4
TitleFAD-dependent oxidoreductase from Chaetomium thermophilum in complex with fragment 4-oxo-N-[(1S)-1-(pyridin-3-yl)ethyl]-4-(thiophen-2-yl)butanamide
ComponentsFAD-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / Chaetomium thermophilum / glucose-methanol-choline oxidoreductase / 4-oxo-N-[(1S)-1-(pyridin-3-yl)ethyl]-4-(thiophen-2-yl)butanamide / fragment screening
Function / homologyChem-479 / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / FORMIC ACID
Function and homology information
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSvecova, L. / Skalova, T. / Kolenko, P. / Koval, T. / Oestergaard, L.H. / Dohnalek, J.
Funding support Czech Republic, 6items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000447 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/16_013/0001776 Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0109 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2015043 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLQ1604 Czech Republic
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum.
Authors: Svecova, L. / Ostergaard, L.H. / Skalova, T. / Schnorr, K.M. / Koval', T. / Kolenko, P. / Stransky, J. / Sedlak, D. / Duskova, J. / Trundova, M. / Hasek, J. / Dohnalek, J.
History
DepositionJun 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 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

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Assembly

Deposited unit
A: FAD-dependent oxidoreductase
B: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,72123
Polymers128,5342
Non-polymers5,18721
Water28,8421601
1
A: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,79212
Polymers64,2671
Non-polymers2,52511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,93011
Polymers64,2671
Non-polymers2,66210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.562, 109.875, 116.113
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FAD-dependent oxidoreductase


Mass: 64267.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The provided sequence corresponds to the mass spectrometry analysis of sample used for crystallization.
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0048040 / Production host: Aspergillus oryzae (mold)

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Sugars , 3 types, 10 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.: 1
Source method: isolated from a genetically manipulated source
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: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
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 , 6 types, 1612 molecules

#4: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-479 / 4-oxo-N-[(1S)-1-(pyridin-3-yl)ethyl]-4-(thiophen-2-yl)butanamide


Mass: 288.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16N2O2S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1601 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17 % (w/v) PEG MME 5000, 0.1 M sodium acetate, pH 5.5, 0.16 M magnesium formate, protein concentration 8 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→49.38 Å / Num. obs: 147085 / % possible obs: 93.5 % / Observed criterion σ(I): -3.7 / Redundancy: 5.5 % / Biso Wilson estimate: 16.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.039 / Rrim(I) all: 0.097 / Net I/σ(I): 8.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.009 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7605 / CC1/2: 0.659 / Rpim(I) all: 0.441 / Rrim(I) all: 1.108 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZE2

6ze2


Resolution: 1.6→49.38 Å / Cor.coef. Fo:Fc: 0.974 / SU B: 1.773 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.092
Details: Hydrogens have been added for refinement in the riding positions. The last refinement cycle was performed against all reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 7299 5 %random selection
Rwork0.1697 146842 --
all0.172 ---
obs0.1722 146842 93.091 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.643 Å2
Baniso -1Baniso -2Baniso -3
1-1.458 Å20 Å2-0 Å2
2---0.984 Å20 Å2
3----0.474 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8917 0 340 1601 10858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139696
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178780
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.67813308
X-RAY DIFFRACTIONr_angle_other_deg1.3771.59220426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22351227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09221.186472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87151451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1581573
X-RAY DIFFRACTIONr_chiral_restr0.0890.21322
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210944
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022057
X-RAY DIFFRACTIONr_nbd_refined0.2020.21944
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.28356
X-RAY DIFFRACTIONr_nbtor_refined0.1660.24736
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23909
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.21154
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.070.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.215
X-RAY DIFFRACTIONr_nbd_other0.1780.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.241
X-RAY DIFFRACTIONr_mcbond_it1.3431.854737
X-RAY DIFFRACTIONr_mcbond_other1.3431.854738
X-RAY DIFFRACTIONr_mcangle_it1.7842.7845938
X-RAY DIFFRACTIONr_mcangle_other1.7852.7845937
X-RAY DIFFRACTIONr_scbond_it1.9782.1334959
X-RAY DIFFRACTIONr_scbond_other1.9762.1324956
X-RAY DIFFRACTIONr_scangle_it2.9013.1197341
X-RAY DIFFRACTIONr_scangle_other2.9013.1197342
X-RAY DIFFRACTIONr_lrange_it4.37224.1811633
X-RAY DIFFRACTIONr_lrange_other4.00123.08311117
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64200.29311366X-RAY DIFFRACTION98.3303
1.642-1.68600.27711061X-RAY DIFFRACTION98.5214
1.686-1.73500.25710827X-RAY DIFFRACTION98.5168
1.735-1.78900.23510413X-RAY DIFFRACTION98.3101
1.789-1.84700.2149940X-RAY DIFFRACTION95.9923
1.847-1.91200.2128232X-RAY DIFFRACTION82.1475
1.912-1.98400.2137898X-RAY DIFFRACTION82.0401
1.984-2.06500.1669145X-RAY DIFFRACTION98.5771
2.065-2.15700.1558835X-RAY DIFFRACTION98.4511
2.157-2.26200.1625229X-RAY DIFFRACTION61.4526
2.262-2.38400.1637613X-RAY DIFFRACTION93.4454
2.384-2.52800.1297623X-RAY DIFFRACTION98.4375
2.528-2.70200.1357108X-RAY DIFFRACTION98.3262
2.702-2.91800.1496657X-RAY DIFFRACTION98.0557
2.918-3.19500.1596108X-RAY DIFFRACTION97.494
3.195-3.5700.165305X-RAY DIFFRACTION93.3322
3.57-4.11900.1574149X-RAY DIFFRACTION82.2235
4.119-5.03600.1334193X-RAY DIFFRACTION97.4436
5.036-7.08600.1563202X-RAY DIFFRACTION94.4543
7.086-49.3800.1881938X-RAY DIFFRACTION96.6584

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