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- PDB-7a0q: Crystal structure of kievitone hydratase from Nectria haematococc... -

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Basic information

Entry
Database: PDB / ID: 7a0q
TitleCrystal structure of kievitone hydratase from Nectria haematococca (C2 SG)
ComponentsCrtC domain-containing protein
KeywordsLYASE / kievitone hydratase / kievitone
Function / homology: / AttH domain / AttH-like domain superfamily / CrtC N-terminal lipocalin domain / Lipocalin-like domain / IMIDAZOLE / AttH domain-containing protein
Function and homology information
Biological speciesFusarium vanettenii 77-13-4 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.5 Å
AuthorsPavkov-Keller, T. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Research Promotion Agency Austria
Citation
Journal: to be published
Title: Structural analysis and reaction mechanism of kievitone hydratase from Nectria haematococca
Authors: Pavkov-Keller, T. / Steinkellner, G. / Engleder, M. / Schuermann, M. / Blasl, H. / Pichler, H. / Gruber, K.
#1: Journal: PLoS ONE / Year: 2018
Title: Recombinant expression, purification and biochemical characterization of kievitone hydratase from Nectria haematococca.
Authors: Engleder, M. / Horvat, M. / Emmerstorfer-Augustin, A. / Wriessnegger, T. / Gabriel, S. / Strohmeier, G. / Weber, H. / Mueller, M. / Kaluzna, I. / Mink, D. / Schuermann, M. / Pichler, H.
History
DepositionAug 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: CrtC domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4786
Polymers38,5861
Non-polymers1,8925
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint25 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.327, 70.201, 51.260
Angle α, β, γ (deg.)90.000, 103.546, 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

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Protein , 1 types, 1 molecules A

#1: Protein CrtC domain-containing protein


Mass: 38586.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium vanettenii 77-13-4 (fungus) / Gene: NECHADRAFT_51190 / Production host: Komagataella pastoris (fungus) / References: UniProt: C7ZKN4

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1_f2-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}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.: 1 / Source method: isolated from a natural 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 , 3 types, 340 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Morpheus 1-2 (0.06 M Divalents: 0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dehydrate; 0.1 M Buffer System 1: 1.0M Imidazole; MES monohydrate pH 6.5, 50% v/v Precipitant Mix 2: ...Details: Morpheus 1-2 (0.06 M Divalents: 0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dehydrate; 0.1 M Buffer System 1: 1.0M Imidazole; MES monohydrate pH 6.5, 50% v/v Precipitant Mix 2: 40% v/v Ethylene glycol; 20% w/v PEG 8000) protein conc. 13-28mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.0396 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0396 Å / Relative weight: 1
ReflectionResolution: 1.5→43.41 Å / Num. obs: 63441 / % possible obs: 94.83 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.11 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Rrim(I) all: 0.067 / Net I/σ(I): 12.17
Reflection shellResolution: 1.5→1.554 Å / Rmerge(I) obs: 0.707 / Num. unique obs: 4943 / CC1/2: 0.602 / CC star: 0.867 / Rpim(I) all: 0.537 / Rrim(I) all: 0.894 / % possible all: 74

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→43.41 Å / SU ML: 0.1883 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.4568
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2081 3170 5 %
Rwork0.1788 60229 -
obs0.1802 63399 94.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.91 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 125 338 3029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062808
X-RAY DIFFRACTIONf_angle_d0.82613845
X-RAY DIFFRACTIONf_chiral_restr0.0551441
X-RAY DIFFRACTIONf_plane_restr0.006481
X-RAY DIFFRACTIONf_dihedral_angle_d3.37212176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.28411020.30661943X-RAY DIFFRACTION70.57
1.52-1.550.34471080.29842045X-RAY DIFFRACTION75.41
1.55-1.570.32281150.27232175X-RAY DIFFRACTION79.51
1.57-1.60.31191230.26172336X-RAY DIFFRACTION83.38
1.6-1.630.3211250.25012384X-RAY DIFFRACTION87.91
1.63-1.660.26481400.24752658X-RAY DIFFRACTION95.85
1.66-1.690.28971440.24382732X-RAY DIFFRACTION99.58
1.69-1.730.27731430.24112707X-RAY DIFFRACTION99.51
1.73-1.770.26081450.22542761X-RAY DIFFRACTION99.49
1.77-1.810.24941430.19852732X-RAY DIFFRACTION99.48
1.81-1.860.2261440.19012733X-RAY DIFFRACTION99.31
1.86-1.920.23411430.18952731X-RAY DIFFRACTION99.48
1.92-1.980.21121440.18112741X-RAY DIFFRACTION99.48
1.98-2.050.2191470.17692789X-RAY DIFFRACTION99.46
2.05-2.130.20321430.17182721X-RAY DIFFRACTION99.51
2.13-2.230.17451460.17622764X-RAY DIFFRACTION99.73
2.23-2.350.1671440.17662739X-RAY DIFFRACTION99.76
2.35-2.50.23281450.18242751X-RAY DIFFRACTION99.31
2.5-2.690.20431450.17842762X-RAY DIFFRACTION99.22
2.69-2.960.18641440.17672732X-RAY DIFFRACTION99.24
2.96-3.390.2191460.16472763X-RAY DIFFRACTION99.15
3.39-4.270.1721430.14852719X-RAY DIFFRACTION97.98
4.27-43.410.18511480.15612811X-RAY DIFFRACTION98.57

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