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- PDB-7ygf: Crystal structure of YggS from Fusobacterium nucleatum -

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Basic information

Entry
Database: PDB / ID: 7ygf
TitleCrystal structure of YggS from Fusobacterium nucleatum
ComponentsPyridoxal phosphate homeostasis protein
KeywordsBIOSYNTHETIC PROTEIN / YggS
Function / homology
Function and homology information


pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Uncharacterized protein family UPF0001 signature. / Pyridoxal phosphate homeostasis protein / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Alanine racemase / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Pyridoxal phosphate homeostasis protein
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsHe, S.R. / Chan, Y.Y. / Wang, L.L. / Bai, X. / Bu, T.T. / Zhang, J. / Xu, Y.B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Molecules / Year: 2022
Title: Structural and Functional Analysis of the Pyridoxal Phosphate Homeostasis Protein YggS from Fusobacterium nucleatum.
Authors: He, S. / Chen, Y. / Wang, L. / Bai, X. / Bu, T. / Zhang, J. / Lu, M. / Ha, N.C. / Quan, C. / Nam, K.H. / Xu, Y.
History
DepositionJul 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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: Pyridoxal phosphate homeostasis protein
B: Pyridoxal phosphate homeostasis protein
C: Pyridoxal phosphate homeostasis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0966
Polymers78,8083
Non-polymers2883
Water9,908550
1
A: Pyridoxal phosphate homeostasis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3652
Polymers26,2691
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-17 kcal/mol
Surface area10920 Å2
MethodPISA
2
B: Pyridoxal phosphate homeostasis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3652
Polymers26,2691
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-19 kcal/mol
Surface area10750 Å2
MethodPISA
3
C: Pyridoxal phosphate homeostasis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3652
Polymers26,2691
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.929, 146.375, 74.128
Angle α, β, γ (deg.)90.000, 93.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pyridoxal phosphate homeostasis protein / PLP homeostasis protein


Mass: 26269.314 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Gene: FN0561 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q8RFW9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 0.1M sodium acetate trihydrate pH4.8, 0.19M Ammonium Sulfate , 21% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→37 Å / Num. obs: 47064 / % possible obs: 97.6 % / Redundancy: 6 % / Biso Wilson estimate: 24.36 Å2 / Rsym value: 0.2 / Net I/σ(I): 27.13
Reflection shellResolution: 2.08→2.154 Å / Mean I/σ(I) obs: 4.333 / Num. unique obs: 1175 / Rsym value: 0.607

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.08→37 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.23 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 1976 4.26 %
Rwork0.1771 44430 -
obs0.1792 46406 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.61 Å2 / Biso mean: 28.3762 Å2 / Biso min: 10.01 Å2
Refinement stepCycle: final / Resolution: 2.08→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5451 0 15 550 6016
Biso mean--35.47 34.83 -
Num. residues----669
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.08-2.13190.25141270.1883278784
2.1319-2.18950.23911320.1915305192
2.1895-2.25390.25811440.1913307994
2.2539-2.32670.26821300.1927312995
2.3267-2.40980.25681430.1829312896
2.4098-2.50630.23271460.1859318196
2.5063-2.62030.23081290.1837317497
2.6203-2.75840.23391470.1911322297
2.7584-2.93120.26421330.1938325597
2.9312-3.15740.22361470.1846322898
3.1574-3.47490.26381450.17333275100
3.4749-3.97730.20131470.15353290100
3.9773-5.0090.17091480.15033316100
5.009-370.23331580.1939331599

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