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- PDB-8erj: Crystal structure of Fub7 in complex with E-2-aminocrotonate -

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Basic information

Entry
Database: PDB / ID: 8erj
TitleCrystal structure of Fub7 in complex with E-2-aminocrotonate
ComponentsSulfhydrylase FUB7
KeywordsBIOSYNTHETIC PROTEIN / C-C bond formation
Function / homology
Function and homology information


transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / transsulfuration / pyridoxal phosphate binding
Similarity search - Function
O-acetylhomoserine/O-acetylserine sulfhydrylase / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-4LM / Chem-WQF / Sulfhydrylase FUB7
Similarity search - Component
Biological speciesFusarium fujikuroi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsHai, Y.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Molecular and Structural Basis for C gamma-C Bond Formation by PLP-Dependent Enzyme Fub7.
Authors: Liu, S. / Yeh, C. / Reavill, C. / Jones, B. / Zou, Y. / Hai, Y.
History
DepositionOct 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfhydrylase FUB7
B: Sulfhydrylase FUB7
C: Sulfhydrylase FUB7
D: Sulfhydrylase FUB7
E: Sulfhydrylase FUB7
F: Sulfhydrylase FUB7
G: Sulfhydrylase FUB7
H: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)396,55016
Polymers393,8968
Non-polymers2,6548
Water19,1141061
1
A: Sulfhydrylase FUB7
hetero molecules

C: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1364
Polymers98,4742
Non-polymers6622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5900 Å2
ΔGint-22 kcal/mol
Surface area29380 Å2
MethodPISA
2
B: Sulfhydrylase FUB7
hetero molecules

D: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1384
Polymers98,4742
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5930 Å2
ΔGint-23 kcal/mol
Surface area29450 Å2
MethodPISA
3
E: Sulfhydrylase FUB7
hetero molecules

G: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1384
Polymers98,4742
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area5920 Å2
ΔGint-23 kcal/mol
Surface area29260 Å2
MethodPISA
4
F: Sulfhydrylase FUB7
H: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1364
Polymers98,4742
Non-polymers6622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-24 kcal/mol
Surface area29210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.957, 194.746, 146.338
Angle α, β, γ (deg.)90.000, 129.318, 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
Components on special symmetry positions
IDModelComponents
11A-623-

HOH

21B-620-

HOH

31C-631-

HOH

41D-624-

HOH

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Components

#1: Protein
Sulfhydrylase FUB7 / Fusaric acid biosynthesis protein 7


Mass: 49236.988 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium fujikuroi (fungus) / Gene: FUB7 / Production host: Escherichia coli (E. coli)
References: UniProt: S0DUX5, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-4LM / (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid


Mass: 330.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-WQF / (2S)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]but-3-enoic acid / Fusaric acid biosynthesis protein 7


Mass: 332.246 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C12H17N2O7P / Feature type: SUBJECT OF INVESTIGATION
References: Transferases; Transferring alkyl or aryl groups, other than methyl groups
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1061 / 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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium malonate pH 6.0, 25% PEG 3350, crystal soaked with 10 mM L-vinylglcyine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→60 Å / Num. obs: 219273 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 26.64 Å2 / CC1/2: 0.993 / Net I/σ(I): 11.8
Reflection shellResolution: 2.15→2.19 Å / Mean I/σ(I) obs: 1.12 / Num. unique obs: 10780 / CC1/2: 0.776

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold

Resolution: 2.16→49.22 Å / SU ML: 0.2266 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2054 11268 5.15 %
Rwork0.1775 207718 -
obs0.179 218986 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.1 Å2
Refinement stepCycle: LAST / Resolution: 2.16→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26454 0 44 1061 27559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008427189
X-RAY DIFFRACTIONf_angle_d0.960336951
X-RAY DIFFRACTIONf_chiral_restr0.06154047
X-RAY DIFFRACTIONf_plane_restr0.00734780
X-RAY DIFFRACTIONf_dihedral_angle_d18.63033773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.180.34242780.31485828X-RAY DIFFRACTION83
2.18-2.210.33323950.28556912X-RAY DIFFRACTION98.84
2.21-2.230.31554030.26196905X-RAY DIFFRACTION99.15
2.23-2.260.29433600.25336972X-RAY DIFFRACTION99.43
2.26-2.290.30313580.24916953X-RAY DIFFRACTION99.35
2.29-2.320.29223810.24296970X-RAY DIFFRACTION99.49
2.32-2.360.28043500.23656978X-RAY DIFFRACTION99.44
2.36-2.390.26793680.23196957X-RAY DIFFRACTION99.46
2.39-2.430.25964460.21026888X-RAY DIFFRACTION99.58
2.43-2.470.26854540.21026882X-RAY DIFFRACTION99.55
2.47-2.510.24743840.2036952X-RAY DIFFRACTION99.58
2.51-2.560.24314070.2056932X-RAY DIFFRACTION99.61
2.56-2.610.23314360.19626932X-RAY DIFFRACTION99.58
2.61-2.660.22713820.1916968X-RAY DIFFRACTION99.39
2.66-2.720.2053460.18487035X-RAY DIFFRACTION99.6
2.72-2.780.21743610.18276977X-RAY DIFFRACTION99.65
2.78-2.850.22093630.18016958X-RAY DIFFRACTION99.55
2.85-2.930.22923540.18577005X-RAY DIFFRACTION99.24
2.93-3.010.1953630.1766919X-RAY DIFFRACTION99.02
3.01-3.110.20413350.17546829X-RAY DIFFRACTION96.73
3.11-3.220.2033630.16966915X-RAY DIFFRACTION99.11
3.22-3.350.20273770.16927020X-RAY DIFFRACTION99.78
3.35-3.50.19573880.16867015X-RAY DIFFRACTION99.93
3.5-3.690.18183770.1587032X-RAY DIFFRACTION99.88
3.69-3.920.16344070.14836968X-RAY DIFFRACTION99.96
3.92-4.220.15153900.14027010X-RAY DIFFRACTION99.96
4.22-4.640.14873940.13287011X-RAY DIFFRACTION99.89
4.64-5.320.15293830.14187040X-RAY DIFFRACTION99.77
5.32-6.690.17243380.16526952X-RAY DIFFRACTION98.06
6.7-49.220.15243270.14197003X-RAY DIFFRACTION97.38

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