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- PDB-6ze5: FAD-dependent oxidoreductase from Chaetomium thermophilum in comp... -

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Basic information

Entry
Database: PDB / ID: 6ze5
TitleFAD-dependent oxidoreductase from Chaetomium thermophilum in complex with fragment 2-(1H-indol-3-yl)-N-[(1-methyl-1H-pyrrol-2-yl)methyl]ethanamine
ComponentsFAD-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / Chaetomium thermophilum / glucose-methanol-choline oxidoreductase / 2-(1H-indol-3-yl)-N-[(1-methyl-1H-pyrrol-2-yl)methyl]ethanamine / fragment screening
Function / homologyChem-4AQ / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / FORMIC ACID
Function and homology information
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 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: FAD-dependent oxidoreductase
B: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,27821
Polymers128,5342
Non-polymers4,74419
Water22,9151272
1
A: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,79012
Polymers64,2671
Non-polymers2,52311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4889
Polymers64,2671
Non-polymers2,2218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.996, 117.013, 109.904
Angle α, β, γ (deg.)90.000, 90.687, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 , 2 types, 8 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.: 2
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
#4: 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.: 6
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 , 5 types, 1283 molecules

#3: 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
#5: Chemical ChemComp-4AQ / 2-(1H-indol-3-yl)-N-[(1-methyl-1H-pyrrol-2-yl)methyl]ethanamine


Mass: 253.342 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H19N3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1272 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
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, 20 mM MgCl2, protein concentration 8 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.82→43.4 Å / Num. obs: 105562 / % possible obs: 99.4 % / Observed criterion σ(I): -3.7 / Redundancy: 3.4 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.051 / Rrim(I) all: 0.094 / Net I/σ(I): 9.6
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 0.673 / Num. unique obs: 5247 / CC1/2: 0.673 / Rpim(I) all: 0.469 / Rrim(I) all: 0.888 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XDSdata scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZE2

6ze2


Resolution: 1.82→43.4 Å / SU ML: 0.1883 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 18.1567
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Hydrogens have been added for refinement in the riding positions. The last refinement cycle was performed against all reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 9615 4.8 %random selection
Rwork0.1666 0 --
obs0.1664 105508 95.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.54 Å2
Refinement stepCycle: LAST / Resolution: 1.82→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8922 0 317 1272 10511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01119648
X-RAY DIFFRACTIONf_angle_d1.127213224
X-RAY DIFFRACTIONf_chiral_restr0.06431485
X-RAY DIFFRACTIONf_plane_restr0.00751704
X-RAY DIFFRACTIONf_dihedral_angle_d19.50333645
LS refinement shell
Resolution (Å)Rfactor RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.840.30720.30726595X-RAY DIFFRACTION95.25
1.84-1.860.30120.30126723X-RAY DIFFRACTION95.01
1.86-1.890.29810.29816696X-RAY DIFFRACTION95.22
1.89-1.910.29010.29016612X-RAY DIFFRACTION95.15
1.91-1.930.28320.28326656X-RAY DIFFRACTION95.18
1.93-1.960.27340.27346671X-RAY DIFFRACTION94.85
1.96-1.990.25640.25646541X-RAY DIFFRACTION94.02
1.99-2.020.25440.25446510X-RAY DIFFRACTION93.07
2.02-2.050.24570.24576691X-RAY DIFFRACTION94.81
2.05-2.080.23450.23456718X-RAY DIFFRACTION96.12
2.08-2.120.23280.23286683X-RAY DIFFRACTION95.61
2.12-2.160.22110.22116673X-RAY DIFFRACTION95.85
2.16-2.20.21250.21256728X-RAY DIFFRACTION96.09
2.2-2.240.21080.21086780X-RAY DIFFRACTION95.9
2.24-2.290.20280.20286605X-RAY DIFFRACTION95.63
2.29-2.350.19580.19586779X-RAY DIFFRACTION95.59
2.35-2.40.18790.18796466X-RAY DIFFRACTION94.31
2.41-2.470.19130.19136643X-RAY DIFFRACTION93.33
2.47-2.540.18260.18266668X-RAY DIFFRACTION96.05
2.54-2.620.18170.18176793X-RAY DIFFRACTION96.26
2.62-2.720.17010.17016659X-RAY DIFFRACTION96.1
2.72-2.830.16280.16286775X-RAY DIFFRACTION96.56
2.83-2.960.15140.15146756X-RAY DIFFRACTION96.29
2.96-3.110.15140.15146648X-RAY DIFFRACTION95.23
3.11-3.310.13970.13976646X-RAY DIFFRACTION95.04
3.31-3.560.1310.1316802X-RAY DIFFRACTION96.94
3.56-3.920.11270.11276800X-RAY DIFFRACTION96.87
3.92-4.490.10370.10376668X-RAY DIFFRACTION96.05
4.49-5.650.10290.10296678X-RAY DIFFRACTION95.52
5.65-43.40.12860.12866745X-RAY DIFFRACTION96.04

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