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- PDB-8eqw: Crystal structure of Fub7 -

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Basic information

Entry
Database: PDB / ID: 8eqw
TitleCrystal structure of Fub7
ComponentsSulfhydrylase FUB7
KeywordsBIOSYNTHETIC PROTEIN / C-C bond formation
Function / homology
Function and homology information


O-acetylhomoserine aminocarboxypropyltransferase activity / L-homocysteine biosynthetic process / cysteine synthase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / transsulfuration / cysteine biosynthetic process from serine / pyridoxal phosphate binding / cytoplasm
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
Biological speciesFusarium fujikuroi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Feb 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 1.3Mar 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


Theoretical massNumber of molelcules
Total (without water)395,7218
Polymers395,7218
Non-polymers00
Water28,0311556
1
A: Sulfhydrylase FUB7
G: Sulfhydrylase FUB7


Theoretical massNumber of molelcules
Total (without water)98,9302
Polymers98,9302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-27 kcal/mol
Surface area29540 Å2
MethodPISA
2
B: Sulfhydrylase FUB7
H: Sulfhydrylase FUB7


Theoretical massNumber of molelcules
Total (without water)98,9302
Polymers98,9302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-26 kcal/mol
Surface area29630 Å2
MethodPISA
3
C: Sulfhydrylase FUB7
E: Sulfhydrylase FUB7


Theoretical massNumber of molelcules
Total (without water)98,9302
Polymers98,9302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-27 kcal/mol
Surface area29500 Å2
MethodPISA
4
D: Sulfhydrylase FUB7
F: Sulfhydrylase FUB7


Theoretical massNumber of molelcules
Total (without water)98,9302
Polymers98,9302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-27 kcal/mol
Surface area29530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.928, 195.295, 112.424
Angle α, β, γ (deg.)90.000, 91.821, 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
Sulfhydrylase FUB7 / Fusaric acid biosynthesis protein 7


Mass: 49465.105 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1556 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium malonate pH 5.6, 22% PEG 3350 / PH range: pH 5-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.195 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: Jan 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.195 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 396744 / % possible obs: 99.9 % / Redundancy: 18.1 % / Biso Wilson estimate: 31.2 Å2 / CC1/2: 0.992 / Net I/σ(I): 43.36
Reflection shellResolution: 1.76→1.8 Å / Redundancy: 14.7 % / Num. unique obs: 19735 / CC1/2: 0.388 / % possible all: 99.9

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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 model

Resolution: 1.76→47.97 Å / SU ML: 0.2564 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.3264
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2286 19813 5.07 %
Rwork0.1978 371321 -
obs0.1994 391134 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.23 Å2
Refinement stepCycle: LAST / Resolution: 1.76→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25854 0 0 1556 27410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011326493
X-RAY DIFFRACTIONf_angle_d1.1435993
X-RAY DIFFRACTIONf_chiral_restr0.06623951
X-RAY DIFFRACTIONf_plane_restr0.00664640
X-RAY DIFFRACTIONf_dihedral_angle_d15.74149398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.31465220.27829392X-RAY DIFFRACTION74.48
1.78-1.80.30386880.260512271X-RAY DIFFRACTION97.59
1.8-1.820.29416920.258212337X-RAY DIFFRACTION98.2
1.82-1.840.30066400.263912618X-RAY DIFFRACTION99.03
1.84-1.870.3766880.338112419X-RAY DIFFRACTION98.69
1.87-1.890.46486310.44311983X-RAY DIFFRACTION94.79
1.89-1.920.49045990.477511401X-RAY DIFFRACTION90.44
1.92-1.950.36696460.312912119X-RAY DIFFRACTION95.6
1.95-1.980.30496570.246512562X-RAY DIFFRACTION99.68
1.98-2.010.28297290.238112587X-RAY DIFFRACTION99.83
2.01-2.050.35496760.303712354X-RAY DIFFRACTION98.11
2.05-2.080.35326420.334412416X-RAY DIFFRACTION97.8
2.08-2.120.26827130.224612555X-RAY DIFFRACTION99.65
2.12-2.170.276320.219312653X-RAY DIFFRACTION99.95
2.17-2.210.27386370.240912394X-RAY DIFFRACTION98.17
2.22-2.270.35315830.319212051X-RAY DIFFRACTION95.07
2.27-2.320.27686930.222112595X-RAY DIFFRACTION99.39
2.32-2.390.25496870.207812645X-RAY DIFFRACTION99.96
2.39-2.460.24076570.197512619X-RAY DIFFRACTION99.88
2.46-2.540.24726550.212686X-RAY DIFFRACTION99.82
2.54-2.630.23726630.202912580X-RAY DIFFRACTION99.65
2.63-2.730.24036730.199212603X-RAY DIFFRACTION99.56
2.73-2.860.23576390.190212707X-RAY DIFFRACTION99.84
2.86-3.010.21976980.18912620X-RAY DIFFRACTION99.88
3.01-3.190.21937050.186312612X-RAY DIFFRACTION99.94
3.19-3.440.2046780.180212654X-RAY DIFFRACTION99.93
3.44-3.790.19636650.174312729X-RAY DIFFRACTION99.95
3.79-4.330.17536890.149412658X-RAY DIFFRACTION99.96
4.33-5.460.17296690.144712726X-RAY DIFFRACTION99.98
5.46-47.970.16476670.159712775X-RAY DIFFRACTION99.36

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