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- PDB-7a0t: Crystal structure of kievitone hydratase from Nectria haematococc... -

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Basic information

Entry
Database: PDB / ID: 7a0t
TitleCrystal structure of kievitone hydratase from Nectria haematococca (P21 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: 2 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. / Muller, 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 1.1Oct 16, 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
B: CrtC domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9757
Polymers77,1732
Non-polymers3,8025
Water7,782432
1
A: CrtC domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3773
Polymers38,5861
Non-polymers1,7912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CrtC domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5984
Polymers38,5861
Non-polymers2,0123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.430, 79.790, 103.180
Angle α, β, γ (deg.)90.000, 100.679, 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

#1: Protein CrtC domain-containing protein


Mass: 38586.422 Da / Num. of mol.: 2
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
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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: 1721.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#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: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: JCSG+ 2-31 (0.1 M Succinic acid, 15% w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2→49 Å / Num. obs: 55149 / % possible obs: 99.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 30.91 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.048 / Rrim(I) all: 0.11 / Net I/σ(I): 11.53
Reflection shellResolution: 2→2.071 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.635 / Num. unique obs: 5469 / CC1/2: 0.715 / CC star: 0.913 / Rpim(I) all: 0.373 / Rrim(I) all: 0.741 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2→49 Å / SU ML: 0.2322 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.8652
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2095 2757 5 %
Rwork0.1761 52360 -
obs0.1778 55117 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.95 Å2
Refinement stepCycle: LAST / Resolution: 2→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5159 0 256 432 5847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00865590
X-RAY DIFFRACTIONf_angle_d0.8837642
X-RAY DIFFRACTIONf_chiral_restr0.0585897
X-RAY DIFFRACTIONf_plane_restr0.0062944
X-RAY DIFFRACTIONf_dihedral_angle_d13.27162042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.33771360.25732573X-RAY DIFFRACTION98.29
2.03-2.070.28291380.22642622X-RAY DIFFRACTION98.92
2.07-2.110.27751370.20982611X-RAY DIFFRACTION99.96
2.11-2.150.25871380.20482617X-RAY DIFFRACTION99.57
2.15-2.20.23521380.20482624X-RAY DIFFRACTION99.93
2.2-2.250.31991370.26192597X-RAY DIFFRACTION99.49
2.25-2.310.34041360.27692591X-RAY DIFFRACTION99.2
2.31-2.370.2441390.20182651X-RAY DIFFRACTION99.75
2.37-2.440.22011380.19012614X-RAY DIFFRACTION99.89
2.44-2.520.26931380.18242612X-RAY DIFFRACTION100
2.52-2.610.23621380.18682623X-RAY DIFFRACTION99.68
2.61-2.710.23861390.18072650X-RAY DIFFRACTION99.54
2.71-2.840.22971370.17732607X-RAY DIFFRACTION99.75
2.84-2.990.19191380.17212607X-RAY DIFFRACTION99.78
2.99-3.170.23771390.17952639X-RAY DIFFRACTION99.64
3.17-3.420.21711380.1682631X-RAY DIFFRACTION98.96
3.42-3.760.16931360.15752581X-RAY DIFFRACTION98.51
3.76-4.310.16781380.14442613X-RAY DIFFRACTION98.29
4.31-5.430.12811380.13092618X-RAY DIFFRACTION98.53
5.43-490.20741410.18482679X-RAY DIFFRACTION98.5

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