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- PDB-8erb: Crystal structure of Fub7 in complex with vinylglycine ketimine -

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Basic information

Entry
Database: PDB / ID: 8erb
TitleCrystal structure of Fub7 in complex with vinylglycine ketimine
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-WBJ / Sulfhydrylase FUB7
Similarity search - Component
Biological speciesFusarium fujikuroi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHai, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
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 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 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 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
G: Sulfhydrylase FUB7
H: Sulfhydrylase FUB7
F: Sulfhydrylase FUB7
I: Sulfhydrylase FUB7
P: Sulfhydrylase FUB7
J: Sulfhydrylase FUB7
M: Sulfhydrylase FUB7
Q: Sulfhydrylase FUB7
N: Sulfhydrylase FUB7
E: Sulfhydrylase FUB7
L: Sulfhydrylase FUB7
K: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)760,17832
Polymers754,89416
Non-polymers5,28416
Water40,8402267
1
A: Sulfhydrylase FUB7
C: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0224
Polymers94,3622
Non-polymers6602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-22 kcal/mol
Surface area29170 Å2
MethodPISA
2
B: Sulfhydrylase FUB7
D: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0224
Polymers94,3622
Non-polymers6602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-26 kcal/mol
Surface area29440 Å2
MethodPISA
3
G: Sulfhydrylase FUB7
hetero molecules

L: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0224
Polymers94,3622
Non-polymers6602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5940 Å2
ΔGint-25 kcal/mol
Surface area29530 Å2
MethodPISA
4
H: Sulfhydrylase FUB7
K: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0224
Polymers94,3622
Non-polymers6602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-26 kcal/mol
Surface area29220 Å2
MethodPISA
5
F: Sulfhydrylase FUB7
P: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0224
Polymers94,3622
Non-polymers6602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-25 kcal/mol
Surface area29280 Å2
MethodPISA
6
I: Sulfhydrylase FUB7
J: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0224
Polymers94,3622
Non-polymers6602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-25 kcal/mol
Surface area29460 Å2
MethodPISA
7
M: Sulfhydrylase FUB7
E: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0224
Polymers94,3622
Non-polymers6602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-24 kcal/mol
Surface area29410 Å2
MethodPISA
8
N: Sulfhydrylase FUB7
hetero molecules

Q: Sulfhydrylase FUB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0224
Polymers94,3622
Non-polymers6602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area5930 Å2
ΔGint-26 kcal/mol
Surface area29160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.703, 193.364, 149.913
Angle α, β, γ (deg.)90.000, 99.600, 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: 47180.879 Da / Num. of mol.: 16
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-WBJ / (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid


Mass: 330.230 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C12H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2267 / 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: 2.81 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium malonate, pH 6.0, 25% PEG 3350, crystals soaked with 2 mM O-acetyl-L-homoserine for 5 min.

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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: 1.98→60 Å / Num. obs: 565830 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 19.83 Å2 / CC1/2: 0.965 / Net I/σ(I): 16.1
Reflection shellResolution: 1.98→2.01 Å / Num. unique obs: 28182 / CC1/2: 0.755

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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: 8EQW

8eqw


Resolution: 1.98→47.75 Å / SU ML: 0.239 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.7055
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2257 28235 5.03 %
Rwork0.2004 533120 -
obs0.2017 561355 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.24 Å2
Refinement stepCycle: LAST / Resolution: 1.98→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52617 0 352 2267 55236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010154324
X-RAY DIFFRACTIONf_angle_d1.254773811
X-RAY DIFFRACTIONf_chiral_restr0.08828083
X-RAY DIFFRACTIONf_plane_restr0.00819557
X-RAY DIFFRACTIONf_dihedral_angle_d12.10327479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-20.28318440.244716790X-RAY DIFFRACTION93.18
2-2.030.27379170.233517899X-RAY DIFFRACTION99.75
2.03-2.050.3199180.279817872X-RAY DIFFRACTION99.38
2.05-2.080.43599010.414317565X-RAY DIFFRACTION97.56
2.08-2.110.33779610.291617653X-RAY DIFFRACTION98.82
2.11-2.140.27489500.220117870X-RAY DIFFRACTION99.82
2.14-2.170.25979170.212218062X-RAY DIFFRACTION99.85
2.17-2.20.24649480.208617832X-RAY DIFFRACTION99.88
2.2-2.230.31639380.272217380X-RAY DIFFRACTION96.98
2.23-2.270.49187990.457816158X-RAY DIFFRACTION89.4
2.27-2.310.2818720.235717763X-RAY DIFFRACTION98.47
2.31-2.350.24279960.198517820X-RAY DIFFRACTION99.89
2.35-2.40.2369560.19517938X-RAY DIFFRACTION99.91
2.4-2.440.21479490.190517962X-RAY DIFFRACTION99.94
2.44-2.50.22249720.188117948X-RAY DIFFRACTION99.93
2.5-2.560.24349930.197817871X-RAY DIFFRACTION99.93
2.56-2.620.23279550.196317945X-RAY DIFFRACTION99.82
2.62-2.690.26619500.2217904X-RAY DIFFRACTION99.7
2.69-2.770.24129500.200917962X-RAY DIFFRACTION99.79
2.77-2.860.22639320.193717919X-RAY DIFFRACTION99.69
2.86-2.960.21989960.197817821X-RAY DIFFRACTION99.56
2.96-3.080.23049500.199617929X-RAY DIFFRACTION99.57
3.08-3.220.20779300.188117906X-RAY DIFFRACTION99.53
3.22-3.390.2129360.189617954X-RAY DIFFRACTION99.48
3.39-3.60.20769820.188617885X-RAY DIFFRACTION99.58
3.6-3.880.19089520.174317881X-RAY DIFFRACTION99.35
3.88-4.270.16399600.151717979X-RAY DIFFRACTION99.66
4.27-4.890.14839680.133418041X-RAY DIFFRACTION99.92
4.89-6.150.167710270.154217992X-RAY DIFFRACTION99.93
6.16-47.750.15019160.147217619X-RAY DIFFRACTION96.35

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