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

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Basic information

Entry
Database: PDB / ID: 6ymh
TitleX-ray structure of the K72I, Y129F, R133L, H199A quadruple mutant of PNP-oxidase from E. coli in complex with PLP
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 / PYRIDOXAL-5'-PHOSPHATE / 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: 2.417 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 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 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
BBB: Pyridoxine/pyridoxamine 5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1406
Polymers50,8842
Non-polymers1,2564
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-44 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.164, 54.164, 271.968
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
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: 0.96828 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96828 Å / Relative weight: 1
ReflectionResolution: 2.417→46.907 Å / Num. obs: 17206 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rpim(I) all: 0.048 / Rrim(I) all: 0.217 / Net I/σ(I): 11.9
Reflection shellResolution: 2.417→2.459 Å / Redundancy: 17.2 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 898 / CC1/2: 0.392 / Rpim(I) all: 0.875 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROC1.0.5 (20190607)data collection
autoPROC1.0.5 (20190607)data processing
XDSVERSION Mar 15, 2019 BUILT=20190315data reduction
XDSVERSION Mar 15, 2019 BUILT=20190315data scaling
AimlessVersion 0.7.4data processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G76

1g76


Resolution: 2.417→46.907 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: FREE R-VALUE / ESU R: 0.398 / ESU R Free: 0.274
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2588 800 4.654 %
Rwork0.1897 --
all0.193 --
obs-17189 99.895 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.324 Å2
Baniso -1Baniso -2Baniso -3
1--1.799 Å2-0.9 Å20 Å2
2---1.799 Å2-0 Å2
3---5.836 Å2
Refinement stepCycle: LAST / Resolution: 2.417→46.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 83 45 3053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133084
X-RAY DIFFRACTIONr_bond_other_d0.0340.0172841
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.6784180
X-RAY DIFFRACTIONr_angle_other_deg2.2371.5946551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8645351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12220.321187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85915525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.911533
X-RAY DIFFRACTIONr_chiral_restr0.1150.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023402
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02720
X-RAY DIFFRACTIONr_nbd_refined0.1810.2572
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22774
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21445
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21542
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.298
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0690.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.215
X-RAY DIFFRACTIONr_nbd_other0.2290.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.27
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0840.21
X-RAY DIFFRACTIONr_mcbond_it3.0556.1321416
X-RAY DIFFRACTIONr_mcbond_other3.0536.1311415
X-RAY DIFFRACTIONr_mcangle_it4.8149.1771763
X-RAY DIFFRACTIONr_mcangle_other4.8149.1781764
X-RAY DIFFRACTIONr_scbond_it3.1696.5641668
X-RAY DIFFRACTIONr_scbond_other3.1636.5621665
X-RAY DIFFRACTIONr_scangle_it5.29.6842417
X-RAY DIFFRACTIONr_scangle_other5.1999.6852418
X-RAY DIFFRACTIONr_lrange_it7.62167.973597
X-RAY DIFFRACTIONr_lrange_other7.62167.983598
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
2.417-2.480.426870.37211960.37512910.3890.47799.38030.373
2.48-2.5470.364450.33911590.3412110.5560.62599.4220.342
2.547-2.6210.331530.31411480.31512030.6540.73199.83370.311
2.621-2.7010.283630.29211280.29211910.8080.7931000.285
2.701-2.790.32420.26610610.26811030.7980.8241000.255
2.79-2.8870.364530.25810490.26311020.7680.8311000.241
2.887-2.9960.349510.21510220.22110730.7850.8781000.196
2.996-3.1180.386440.2159550.2219990.7990.8871000.195
3.118-3.2560.267360.1999380.2029740.9010.9121000.185
3.256-3.4140.341350.1829200.1879550.8410.9281000.164
3.414-3.5970.249500.1778390.1818890.9140.9411000.165
3.597-3.8140.183470.1617710.1638180.9390.9531000.154
3.814-4.0750.268260.1657780.1678040.8980.9471000.156
4.075-4.3990.242210.1487000.1517210.9250.9541000.145
4.399-4.8150.205230.1416540.1436770.9480.9541000.14
4.815-5.3760.163290.1525900.1526190.9560.9521000.152
5.376-6.1940.297370.1785110.1865480.8950.931000.177
6.194-7.5540.252200.1894410.1924610.9050.9271000.191
7.554-10.5460.181300.1483250.1513550.9530.9621000.165
10.546-46.9070.36580.2082030.2132120.920.94899.52830.229

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