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- PDB-5t1f: Crystal structure of Phaeospaeria nodrum fructosyl peptide oxidas... -

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Basic information

Entry
Database: PDB / ID: 5t1f
TitleCrystal structure of Phaeospaeria nodrum fructosyl peptide oxidase mutant Asn56Ala
ComponentsUncharacterized protein
KeywordsOXIDOREDUCTASE / Fructosyl peptide oxidase / FAD
Function / homology
Function and homology information


saccharopine oxidase activity / sarcosine oxidase activity / flavin adenine dinucleotide binding
Similarity search - Function
MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / FAD dependent oxidoreductase domain-containing protein
Similarity search - Component
Biological speciesPhaeosphaeria nodorum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsYoshida, H. / Shimasaki, T. / Kamitori, S. / Sode, K.
Citation
Journal: Sci Rep / Year: 2017
Title: X-ray structures of fructosyl peptide oxidases revealing residues responsible for gating oxygen access in the oxidative half reaction
Authors: Shimasaki, T. / Yoshida, H. / Kamitori, S. / Sode, K.
#1: Journal: Biotechnol. Bioeng. / Year: 2010
Title: Motif-based search for a novel fructosyl peptide oxidase from genome databases.
Authors: Kim, S. / Ferri, S. / Tsugawa, W. / Mori, K. / Sode, K.
History
DepositionAug 19, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9033
Polymers49,0581
Non-polymers8462
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-11 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.579, 93.327, 47.756
Angle α, β, γ (deg.)90.00, 98.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 49057.516 Da / Num. of mol.: 1 / Mutation: N56A
Source method: isolated from a genetically manipulated source
Details: N56A mutant
Source: (gene. exp.) Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) (fungus)
Strain: SN15 / ATCC MYA-4574 / FGSC 10173 / Gene: SNOG_08398 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0UIL6
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
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: 1.96 Å3/Da / Density % sol: 37.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 8%(w/v) Tacsimate, 18-22%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 24157 / % possible obs: 91.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.8
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2 / % possible all: 84.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T1E

5t1e


Resolution: 1.98→39.14 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.146 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.161 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19535 1226 5.1 %RANDOM
Rwork0.15792 ---
obs0.15987 22908 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0.03 Å2
2--0.04 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.98→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 57 220 3607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193485
X-RAY DIFFRACTIONr_bond_other_d00.023243
X-RAY DIFFRACTIONr_angle_refined_deg0.8471.9634740
X-RAY DIFFRACTIONr_angle_other_deg0.51537472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9545432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96223.856153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13815551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4581520
X-RAY DIFFRACTIONr_chiral_restr0.0530.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213956
X-RAY DIFFRACTIONr_gen_planes_other00.02808
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 78 -
Rwork0.27 1504 -
obs--83.75 %

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