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- PDB-6yji: Structure of FgCelDH7C -

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Basic information

Entry
Database: PDB / ID: 6yji
TitleStructure of FgCelDH7C
ComponentsFAD-binding PCMH-type domain-containing protein
KeywordsOXIDOREDUCTASE / FAD / linking
Function / homology
Function and homology information


FAD binding / oxidoreductase activity
Similarity search - Function
Berberine/berberine-like / Berberine and berberine like / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / FAD-binding PCMH-type domain-containing protein
Similarity search - Component
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsHaddad Momeni, M. / Fredslund, F. / Berrin, J.G. / Abou Hachem, M. / Welner, D.H.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0025642 Denmark
CitationJournal: Nat Commun / Year: 2021
Title: Discovery of fungal oligosaccharide-oxidising flavo-enzymes with previously unknown substrates, redox-activity profiles and interplay with LPMOs.
Authors: Haddad Momeni, M. / Fredslund, F. / Bissaro, B. / Raji, O. / Vuong, T.V. / Meier, S. / Nielsen, T.S. / Lombard, V. / Guigliarelli, B. / Biaso, F. / Haon, M. / Grisel, S. / Henrissat, B. / ...Authors: Haddad Momeni, M. / Fredslund, F. / Bissaro, B. / Raji, O. / Vuong, T.V. / Meier, S. / Nielsen, T.S. / Lombard, V. / Guigliarelli, B. / Biaso, F. / Haon, M. / Grisel, S. / Henrissat, B. / Welner, D.H. / Master, E.R. / Berrin, J.G. / Abou Hachem, M.
History
DepositionApr 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.identifier_ORCID / _audit_author.name ..._audit_author.identifier_ORCID / _audit_author.name / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.title / _citation.year
Revision 1.2Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Apr 28, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAD-binding PCMH-type domain-containing protein
B: FAD-binding PCMH-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,09123
Polymers106,5762
Non-polymers4,51521
Water17,042946
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A: FAD-binding PCMH-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,50412
Polymers53,2881
Non-polymers2,21711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FAD-binding PCMH-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,58711
Polymers53,2881
Non-polymers2,29910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.536, 187.821, 55.447
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FAD-binding PCMH-type domain-containing protein


Mass: 53287.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (fungus)
Strain: PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084 / Gene: FG08824.1, FGRAMPH1_01T10923 / Production host: Komagataella pastoris (fungus) / References: UniProt: I1RWY4

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Sugars , 2 types, 6 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: 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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / 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 , 7 types, 961 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CNS
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 946 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 20% (w/v) Sodium thiocyanate 100 mM / Temp details: Non-controlled room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976253 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2019 / Details: KB mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976253 Å / Relative weight: 1
ReflectionResolution: 1.64→53.18 Å / Num. obs: 119235 / % possible obs: 95.55 % / Redundancy: 13 % / Biso Wilson estimate: 22.67 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1827 / Rpim(I) all: 0.05181 / Net I/σ(I): 6.22
Reflection shellResolution: 1.64→1.699 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.547 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 9035 / CC1/2: 0.728 / CC star: 0.918 / Rpim(I) all: 0.5036 / % possible all: 73.16

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K8E

5k8e


Resolution: 1.64→53.18 Å / SU ML: 0.1826 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.7288
RfactorNum. reflection% reflection
Rfree0.2008 5910 4.97 %
Rwork0.1637 --
obs0.1656 118799 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.36 Å2
Refinement stepCycle: LAST / Resolution: 1.64→53.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7322 0 290 946 8558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097973
X-RAY DIFFRACTIONf_angle_d1.020510854
X-RAY DIFFRACTIONf_chiral_restr0.05771175
X-RAY DIFFRACTIONf_plane_restr0.00691384
X-RAY DIFFRACTIONf_dihedral_angle_d13.72682856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.660.22641310.25222626X-RAY DIFFRACTION67.74
1.66-1.680.29951260.25042832X-RAY DIFFRACTION72.01
1.68-1.70.29421610.24712983X-RAY DIFFRACTION77.19
1.7-1.720.3031690.24913207X-RAY DIFFRACTION81.43
1.72-1.740.26981500.23363368X-RAY DIFFRACTION86.23
1.74-1.770.2891880.22893662X-RAY DIFFRACTION94.16
1.77-1.790.25022280.21643840X-RAY DIFFRACTION97.86
1.79-1.820.27751910.20953797X-RAY DIFFRACTION98.4
1.82-1.850.23522000.19753874X-RAY DIFFRACTION98.52
1.85-1.880.21982080.1963808X-RAY DIFFRACTION98.48
1.88-1.910.25362070.18533873X-RAY DIFFRACTION98.53
1.91-1.940.22622040.17963818X-RAY DIFFRACTION98.6
1.94-1.980.21792100.17693921X-RAY DIFFRACTION98.85
1.98-2.020.19972290.17663823X-RAY DIFFRACTION98.93
2.02-2.060.22041900.1713889X-RAY DIFFRACTION98.93
2.06-2.110.23561890.17633894X-RAY DIFFRACTION99.25
2.11-2.170.17731870.16493902X-RAY DIFFRACTION99.46
2.17-2.220.20092020.16113949X-RAY DIFFRACTION99.35
2.22-2.290.19631990.16053889X-RAY DIFFRACTION99.49
2.29-2.360.2131950.15743930X-RAY DIFFRACTION99.49
2.36-2.450.18522210.15253896X-RAY DIFFRACTION99.71
2.45-2.550.22152170.15663938X-RAY DIFFRACTION99.66
2.55-2.660.2221860.15473973X-RAY DIFFRACTION99.81
2.66-2.80.2022090.16043950X-RAY DIFFRACTION99.88
2.8-2.980.20791930.16583959X-RAY DIFFRACTION99.9
2.98-3.210.20622020.16854004X-RAY DIFFRACTION99.9
3.21-3.530.19722190.15883977X-RAY DIFFRACTION99.95
3.53-4.040.18112210.14234030X-RAY DIFFRACTION100
4.04-5.090.16112410.12764061X-RAY DIFFRACTION100
5.09-53.180.18562370.16964216X-RAY DIFFRACTION99.6
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)
10.440712712354-0.1726832402450.6075544437350.0655294236759-0.2200428809720.917126822267-0.214414898175-0.1518294101670.402471405363-0.248019297648-0.1334615559650.916501435194-0.343525093164-0.4481329711880.08495064999980.370941351110.100350973172-0.2770361192230.291184300086-0.063521342320.818211216543-41.292374630139.830718096116.8274488772
20.9758222129890.1696205832450.2377495210771.30773486240.2614119647570.455585750118-0.1057267201540.07509110597620.20462277725-0.239918700257-0.03940809986220.450282177911-0.104266002999-0.0628493823720.07116097131810.205470855720.0136727943631-0.07688435834790.176235488854-0.005564225693910.297606688554-31.340216401921.627483478217.3217692595
31.020503221460.533636311305-0.005812257870261.64104031927-0.8659537394442.19689426862-0.1097989635840.2097596836930.0272786229362-0.5455485038950.05080141380550.2714077343010.0174177159020.1208969077920.03393083468560.257291894770.00152530307537-0.06470137424150.205352682873-0.01720482874990.178373930201-23.977266864418.198230333111.7943814632
41.000399273740.3537960959120.5017865433841.901244237390.758427043391.43206350560.0318864182384-0.245476720562-0.07434658145530.303600418092-0.075945313745-0.15401715980.1047884129080.1260073288090.0279027511280.3261868467950.0025894523069-0.01378414193870.2709708003820.02210069743470.164184266399-10.556004573515.794652175444.3151735643
51.075037386560.5430437128870.3750668179961.707251526380.2004259797320.7963497916610.0524518568019-0.09149148547580.01198850980490.173371315923-0.07857008862240.1177075685550.0116583340863-0.001598425894040.03485568591210.1831633770440.01297713995750.02975667132750.200180522677-0.003719639297520.12957647535-15.94802852822.448272264735.6512348749
63.14240480595-0.678527962191.613563850051.49558585987-0.7219474836215.09402442792-0.1804910504650.3431823075760.149714713461-0.4385992836310.0227407504210.162710142454-0.4152181150130.3616662367520.1613188302030.333902493391-0.0601449288671-0.0534454912280.2164217450740.03326073379540.19213718623-16.153322972435.298581367111.9596253465
72.979514830840.7025391269660.3459908770132.25577211777-0.2463171427131.93460009471-0.08120057835510.251816158465-0.359121276398-0.7262131120420.1577332616210.2616840964560.720106579536-0.459922863207-0.08380401835540.53897607635-0.0907715499715-0.08225286567680.311216637792-0.03272423371440.30243591922911.0977252672-2.105835872238.53210067378
81.775701977570.330779594401-0.4113188799661.651797477260.4046936400041.52922128842-0.001699671727270.231326443309-0.142219279382-0.20547813492-0.001718272577040.0471494761990.157405933713-0.0815389897406-0.00384807427520.2388990700330.0234439961413-0.01553468695250.1883322878790.02483811354430.18954428986219.82210700199.3385943925710.9947526707
90.657957733929-0.0808154752099-0.06907869200090.5866035590480.2544455141840.6691643565960.05025980401230.003078686316150.0795993542842-0.05317848633130.0444891669309-0.195213962096-0.04461215132980.0840645303593-0.1059491422040.1769283020850.0002823827763760.03895241564240.1624735382850.01273936691410.28122440563433.629806124924.125056625525.4649630875
100.908981017729-0.0781050606829-0.08655794484750.6699673066880.1897416959430.8808012575560.07377706359960.04846931342150.166949971863-0.120648265026-0.0214138526425-0.0875825967307-0.101997039165-0.060772324194-0.03330052222830.2147366395560.02502243611690.02421305350950.2030120344810.04813270978750.29275678504616.230370521229.517891362924.0724872314
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 180 )
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 233 )
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 261 )
5X-RAY DIFFRACTION5chain 'A' and (resid 262 through 460 )
6X-RAY DIFFRACTION6chain 'A' and (resid 461 through 499 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 52 )
8X-RAY DIFFRACTION8chain 'B' and (resid 53 through 128 )
9X-RAY DIFFRACTION9chain 'B' and (resid 129 through 348 )
10X-RAY DIFFRACTION10chain 'B' and (resid 349 through 499 )

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