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- PDB-6ylz: X-ray structure of the K72I,Y129F,R133L, H199A quadruple mutant o... -

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Basic information

Entry
Database: PDB / ID: 6ylz
TitleX-ray structure of the K72I,Y129F,R133L, H199A quadruple mutant of PNP-oxidase from E. coli
ComponentsPyridoxine/pyridoxamine 5'-phosphate oxidase
KeywordsFLAVOPROTEIN / Pyridoxal 5'-phosphate / Vitamine B6 metabolism / oxidase
Function / homology
Function and homology information


'de novo' pyridoxal 5'-phosphate biosynthetic process / pyridoxal 5'-phosphate synthase / pyridoxamine phosphate oxidase activity / riboflavin binding / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / phosphate ion binding / pyridoxal phosphate binding / FMN binding / oxidoreductase activity ...'de novo' pyridoxal 5'-phosphate biosynthetic process / pyridoxal 5'-phosphate synthase / pyridoxamine phosphate oxidase activity / riboflavin binding / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / phosphate ion binding / pyridoxal phosphate binding / FMN binding / oxidoreductase activity / protein homodimerization activity / protein-containing complex / cytosol
Similarity search - Function
Pyridoxamine 5'-phosphate oxidase, conserved site / Pyridoxamine 5'-phosphate oxidase signature. / Pyridoxamine 5'-phosphate oxidase / Pyridoxine 5'-phosphate oxidase, dimerisation, C-terminal / Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / FMN-binding split barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Pyridoxine/pyridoxamine 5'-phosphate oxidase / Pyridoxine/pyridoxamine 5'-phosphate oxidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.558 Å
AuthorsBattista, T. / Sularea, M. / Barile, A. / Fiorillo, A. / Tramonti, A. / Ilari, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Other governmentCUP B86C17000270001 Italy
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Identification and characterization of the pyridoxal 5'-phosphate allosteric site in Escherichia coli pyridoxine 5'-phosphate oxidase.
Authors: Barile, A. / Battista, T. / Fiorillo, A. / di Salvo, M.L. / Malatesta, F. / Tramonti, A. / Ilari, A. / Contestabile, R.
History
DepositionApr 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / entity / entity_src_gen / pdbx_database_proc / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_mutation / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Pyridoxine/pyridoxamine 5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1865
Polymers25,4421
Non-polymers7434
Water3,135174
1
AAA: Pyridoxine/pyridoxamine 5'-phosphate oxidase
hetero molecules

AAA: Pyridoxine/pyridoxamine 5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,37110
Polymers50,8842
Non-polymers1,4878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8330 Å2
ΔGint-93 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.776, 63.776, 124.727
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Pyridoxine/pyridoxamine 5'-phosphate oxidase / PNP/PMP oxidase / PNPOx / Pyridoxal 5'-phosphate synthase


Mass: 25442.062 Da / Num. of mol.: 1 / Mutation: K72I, Y129F, R133L, H199A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: pdxH, b1638, JW1630 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AFI7, UniProt: E2QMK2*PLUS, pyridoxal 5'-phosphate synthase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM KPHO pH 7,5, 5 mM 2-mercaptoethanol, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.558→55.233 Å / Num. obs: 41877 / % possible obs: 98 % / Redundancy: 19.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.03 / Rrim(I) all: 0.134 / Net I/σ(I): 13.6
Reflection shellResolution: 1.558→1.585 Å / Redundancy: 11.91 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2040 / CC1/2: 0.444 / Rpim(I) all: 0.803 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCVERSION Mar 15, 2019 BUILT=20191211data collection
autoPROC1.0.5data processing
XDSVERSION Mar 15, 2019 BUILT=20191211data reduction
XDSVERSION Mar 15, 2019 BUILT=20191211data scaling
AimlessVersion 0.7.4data processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G76

1g76


Resolution: 1.558→55.232 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.865 / SU ML: 0.061 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2022 2061 4.953 %
Rwork0.1706 --
all0.172 --
obs-41608 97.351 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.778 Å20.389 Å20 Å2
2--0.778 Å2-0 Å2
3----2.524 Å2
Refinement stepCycle: LAST / Resolution: 1.558→55.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 46 174 1968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131983
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171825
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.6652718
X-RAY DIFFRACTIONr_angle_other_deg1.4281.5854246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0825250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33620.894123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68515355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1851520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022237
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02461
X-RAY DIFFRACTIONr_nbd_refined0.2720.2354
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21701
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2902
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2926
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2142
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.217
X-RAY DIFFRACTIONr_nbd_other0.1930.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.217
X-RAY DIFFRACTIONr_mcbond_it3.0173.21896
X-RAY DIFFRACTIONr_mcbond_other3.0083.21895
X-RAY DIFFRACTIONr_mcangle_it4.1784.81131
X-RAY DIFFRACTIONr_mcangle_other4.1814.81132
X-RAY DIFFRACTIONr_scbond_it4.0363.6461087
X-RAY DIFFRACTIONr_scbond_other3.9723.6351074
X-RAY DIFFRACTIONr_scangle_it6.0755.2871570
X-RAY DIFFRACTIONr_scangle_other6.0615.2621553
X-RAY DIFFRACTIONr_lrange_it8.0836.4552357
X-RAY DIFFRACTIONr_lrange_other7.99435.7792309
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.558-1.5990.3631430.36526430.36531100.5810.57589.5820.355
1.599-1.6430.31440.32228590.32130320.6820.67399.04350.307
1.643-1.690.2761620.27527840.27529510.7630.77199.83060.25
1.69-1.7420.2751490.25127050.25228550.8160.83799.9650.222
1.742-1.7990.2611470.21126280.21327750.8740.8911000.184
1.799-1.8620.2061370.18925590.1926970.9180.92699.96290.163
1.862-1.9320.1981180.17725110.17826290.9420.9461000.153
1.932-2.0110.1841010.15924160.1625170.9520.9571000.139
2.011-2.1010.189850.17416410.17424020.9350.94671.85680.151
2.101-2.2030.1981260.15722060.15923330.9530.96299.95710.144
2.203-2.3220.1981060.15220790.15421860.9490.96199.95430.14
2.322-2.4630.199980.14820000.15120980.9550.9661000.137
2.463-2.6320.1971030.14818710.1519740.9610.9691000.14
2.632-2.8430.172880.14717390.14918270.9670.9691000.147
2.843-3.1130.187850.15216250.15417110.9580.96799.94160.155
3.113-3.4790.223700.1613980.16315520.9420.96194.58760.17
3.479-4.0150.194640.15913320.16113960.9620.9681000.178
4.015-4.910.167650.12611130.12911790.9740.97999.91520.153
4.91-6.9170.2410.1839020.1839430.9690.9681000.218
6.917-55.2320.201290.2235350.2225660.9540.95799.64660.294

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