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- PDB-7f3v: Crystal structure of YfiH with C107A mutation in complex with end... -

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Basic information

Entry
Database: PDB / ID: 7f3v
TitleCrystal structure of YfiH with C107A mutation in complex with endogenous UDP-MurNAc
ComponentsPurine nucleoside phosphorylase YfiH
KeywordsHYDROLASE / DUF152 / amidase
Function / homology
Function and homology information


Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor / 2'-deoxyadenosine deaminase activity / adenosine deaminase / S-methyl-5'-thioadenosine phosphorylase / adenosine deaminase activity / S-methyl-5-thioadenosine phosphorylase activity / peptidoglycan metabolic process / purine-nucleoside phosphorylase / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / purine-nucleoside phosphorylase activity ...Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor / 2'-deoxyadenosine deaminase activity / adenosine deaminase / S-methyl-5'-thioadenosine phosphorylase / adenosine deaminase activity / S-methyl-5-thioadenosine phosphorylase activity / peptidoglycan metabolic process / purine-nucleoside phosphorylase / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / purine-nucleoside phosphorylase activity / outer membrane-bounded periplasmic space / copper ion binding / protein homodimerization activity / cytosol
Similarity search - Function
Multi-copper polyphenol oxidoreductase / Multi-copper polyphenol oxidoreductase superfamily / Multi-copper polyphenol oxidoreductase laccase / Cytotoxic necrotizing factor-like, catalytic
Similarity search - Domain/homology
Chem-EPZ / PHOSPHATE ION / Purine nucleoside phosphorylase YfiH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsLee, M.S. / Hsieh, K.Y. / Chang, C.I.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
Citation
Journal: Mbio / Year: 2021
Title: Structural Basis for the Peptidoglycan-Editing Activity of YfiH.
Authors: Lee, M.S. / Hsieh, K.Y. / Kuo, C.I. / Lee, S.H. / Garde, S. / Reddy, M. / Chang, C.I.
#1: Journal: Biorxiv / Year: 2021
Title: Structural basis for the peptidoglycan editing activity of YfiH
Authors: Lee, M.S. / Hsieh, K.Y. / Kuo, C.I. / Lee, S.H. / Chang, C.I.
History
DepositionJun 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 8, 2023Group: Database references / Category: citation / Item: _citation.year
Revision 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase YfiH
B: Purine nucleoside phosphorylase YfiH
C: Purine nucleoside phosphorylase YfiH
D: Purine nucleoside phosphorylase YfiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,78012
Polymers109,6284
Non-polymers3,1528
Water15,097838
1
A: Purine nucleoside phosphorylase YfiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1813
Polymers27,4071
Non-polymers7742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10450 Å2
MethodPISA
2
B: Purine nucleoside phosphorylase YfiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1813
Polymers27,4071
Non-polymers7742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-6 kcal/mol
Surface area10040 Å2
MethodPISA
3
C: Purine nucleoside phosphorylase YfiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2093
Polymers27,4071
Non-polymers8022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10290 Å2
MethodPISA
4
D: Purine nucleoside phosphorylase YfiH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2093
Polymers27,4071
Non-polymers8022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.949, 98.831, 136.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Purine nucleoside phosphorylase YfiH / Adenosine deaminase YfiH / Polyphenol oxidase YfiH / S-methyl-5'-thioadenosine phosphorylase YfiH


Mass: 27406.998 Da / Num. of mol.: 4 / Mutation: C107A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P33644, adenosine deaminase
#2: Chemical
ChemComp-EPZ / (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid


Mass: 679.416 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H31N3O19P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 838 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 2M ammonium sulfate, 100 mM sodium phosphate at pH 5.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 149115 / % possible obs: 97.3 % / Redundancy: 6.9 % / CC1/2: 0.965 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.017 / Net I/σ(I): 40.08
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 10787 / CC1/2: 0.854 / Rpim(I) all: 0.27 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z9T

1z9t


Resolution: 1.47→34.08 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.381 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 7531 5 %RANDOM
Rwork0.1852 ---
obs0.1866 141889 92.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.57 Å2 / Biso mean: 16.416 Å2 / Biso min: 6.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0 Å2
2---0.12 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.47→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7277 0 202 838 8317
Biso mean--14.61 26.32 -
Num. residues----955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0137679
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177101
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.64810467
X-RAY DIFFRACTIONr_angle_other_deg1.5081.57916333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915953
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84621.32394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.146151150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9511557
X-RAY DIFFRACTIONr_chiral_restr0.0930.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021799
LS refinement shellResolution: 1.47→1.505 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.28 356 -
Rwork0.255 7130 -
obs--63.23 %

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