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- PDB-7f8e: Crystal structure of YggS from Fusobacterium nucleatum -

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Basic information

Entry
Database: PDB / ID: 7f8e
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsWang, L. / Chen, Y. / Bu, T. / Bai, X.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017R1D1A1B03033087 Korea, Republic Of
National Research Foundation (NRF, Korea)2017M3A9F6029736 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of YggS from Fusobacterium nucleatum
Authors: Wang, L. / Chen, Y.
History
DepositionJul 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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

Downloads & links

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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)78,9256
Polymers78,6373
Non-polymers2883
Water10,413578
1
A: Pyridoxal phosphate homeostasis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3082
Polymers26,2121
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10800 Å2
MethodPISA
2
B: Pyridoxal phosphate homeostasis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3082
Polymers26,2121
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-19 kcal/mol
Surface area10620 Å2
MethodPISA
3
C: Pyridoxal phosphate homeostasis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3082
Polymers26,2121
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.929, 146.375, 74.128
Angle α, β, γ (deg.)90.000, 93.355, 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 Pyridoxal phosphate homeostasis protein / YggS family pyridoxal phosphate-dependent enzyme / PLP homeostasis protein


Mass: 26212.266 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355) (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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.65 Å3/Da / Density % sol: 53.5 %
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: 0.9793 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: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.08→36.59 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→36.59 Å / SU ML: 0.2258 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.9099
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2191 1980 4.26 %
Rwork0.1722 44457 -
obs0.1742 46437 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.68 Å2
Refinement stepCycle: LAST / Resolution: 2.08→36.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5406 0 15 578 5999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815552
X-RAY DIFFRACTIONf_angle_d0.87267442
X-RAY DIFFRACTIONf_chiral_restr0.052842
X-RAY DIFFRACTIONf_plane_restr0.0046932
X-RAY DIFFRACTIONf_dihedral_angle_d3.73164903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.24421270.17972789X-RAY DIFFRACTION84.45
2.13-2.190.23871320.18523050X-RAY DIFFRACTION92.23
2.19-2.250.26141450.18513089X-RAY DIFFRACTION93.96
2.25-2.330.25611300.18323130X-RAY DIFFRACTION95.21
2.33-2.410.26711430.17813131X-RAY DIFFRACTION95.73
2.41-2.510.24231470.1723184X-RAY DIFFRACTION96.11
2.51-2.620.24711300.17483177X-RAY DIFFRACTION96.67
2.62-2.760.22431470.18133224X-RAY DIFFRACTION97.09
2.76-2.930.25031340.18313259X-RAY DIFFRACTION97.61
2.93-3.160.22661470.17883228X-RAY DIFFRACTION98.17
3.16-3.470.24951450.16583275X-RAY DIFFRACTION99.53
3.47-3.980.18551470.1543292X-RAY DIFFRACTION99.88
3.98-5.010.14931480.14833315X-RAY DIFFRACTION99.6
5.01-5.010.2281580.19593314X-RAY DIFFRACTION99

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