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- PDB-6yjo: Structure of FgChi7B -

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Basic information

Entry
Database: PDB / ID: 6yjo
TitleStructure of FgChi7B
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, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FAD-binding PCMH-type domain-containing protein
Similarity search - Component
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 2.0Mar 31, 2021Group: Atomic model / Database references / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / citation / citation_author
Item: _atom_site_anisotrop.id / _audit_author.name ..._atom_site_anisotrop.id / _audit_author.name / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.title / _citation.year
Revision 2.1Apr 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 2.2Apr 28, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.3Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6583
Polymers56,2861
Non-polymers1,3722
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint1 kcal/mol
Surface area18310 Å2
Unit cell
Length a, b, c (Å)111.600, 67.455, 85.082
Angle α, β, γ (deg.)90.000, 116.310, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 56285.500 Da / Num. of mol.: 1
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: FGRAMPH1_01T15319 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A098DND1
#2: 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
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: PEG 3350, 22% (w/v) Sodium potassium phosphate, 200 mM
Temp details: Room temp

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 2, 2018 / Details: CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.38→38.13 Å / Num. obs: 22534 / % possible obs: 98.3 % / Redundancy: 7.3 % / Biso Wilson estimate: 46.96 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1385 / Rpim(I) all: 0.05467 / Net I/σ(I): 10.79
Reflection shellResolution: 2.38→2.465 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.573 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 2206 / CC1/2: 0.454 / CC star: 0.79 / Rpim(I) all: 0.6205 / % possible all: 97.35

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDS20180106data reduction
XSCALE20180106data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K8E

5k8e


Resolution: 2.38→38.13 Å / SU ML: 0.3688 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.5617
RfactorNum. reflection% reflection
Rfree0.2376 1116 4.96 %
Rwork0.2123 --
obs0.2137 22501 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 58.36 Å2
Refinement stepCycle: LAST / Resolution: 2.38→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 92 110 3870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323862
X-RAY DIFFRACTIONf_angle_d0.66475266
X-RAY DIFFRACTIONf_chiral_restr0.0448579
X-RAY DIFFRACTIONf_plane_restr0.0041666
X-RAY DIFFRACTIONf_dihedral_angle_d15.82351363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.490.36031270.34722651X-RAY DIFFRACTION97.85
2.49-2.620.34751330.30862690X-RAY DIFFRACTION98.95
2.62-2.780.3331190.28722660X-RAY DIFFRACTION98.48
2.78-30.32351430.27542651X-RAY DIFFRACTION98.55
3-3.30.27921280.25462659X-RAY DIFFRACTION96.97
3.3-3.780.23871730.20262572X-RAY DIFFRACTION96.21
3.78-4.760.16841420.15892733X-RAY DIFFRACTION100
4.76-38.130.20371510.17082769X-RAY DIFFRACTION99.73
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)
11.70335220411.729566432470.1673303373213.140697104970.2308284871741.04147651475-0.3768909828480.577134329725-0.082819348592-0.383920643860.516929632555-0.369761196471-0.06475129940410.17109307778-0.1343999261620.410011789519-0.1034136400660.06492299255910.537454581474-0.06685291845430.36322757654913.955523653136.792894117713.4120272328
21.706072790210.822770540047-0.162805712574.31176324496-0.3944677850051.8977502903-0.379168006240.384024019375-0.0267273196867-0.946630721070.4484154514710.4206704356570.2277572421710.0294254071111-0.1170942930560.613737286253-0.220317099617-0.07541880155510.6377671265480.05307908303410.40853280738-4.2766554988722.05103953379.16149651014
31.080763738450.670276643473-1.375964888932.45765749697-1.735745046633.01169097142-0.2793481217560.4940702144930.5528303346680.4739426234290.3266984492920.874453515512-0.318811725224-0.7282294215440.09277146771210.4710065051580.0397920251312-0.08088625787820.5760117257620.2246937523231.52432330737-23.110401078138.476259043720.4467409258
41.829742477731.903445437810.1949066889234.01242501305-0.02248335371511.32739793868-0.05801196591080.1832182714840.2941382405640.4735805627520.2323983043580.3987440848340.0264176840534-0.0793630304599-0.1794900450910.4115804315970.03263850191120.06622066124930.3452793729520.04512913981190.31544640022-4.3840538957928.730085778826.0997300637
51.64086723531.84295335522-0.3310247724833.420360217570.2692419092231.521604949040.00627620080751-0.0523318383126-0.2396461933480.6735927352210.183821449472-0.705249887965-0.06292348600320.232834427968-0.1876562953440.5011019692260.0359107062716-0.1295851745710.33260567535-0.04542470916850.38030504315418.757225926340.786281839328.2828940333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 357 through 475 )
2X-RAY DIFFRACTION2chain 'A' and (resid 476 through 505 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 58 )
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 240 )
5X-RAY DIFFRACTION5chain 'A' and (resid 241 through 356 )

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