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

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Basic information

Entry
Database: PDB / ID: 5xao
TitleCrystal structure of Phaeospaeria nodrum fructosyl peptide oxidase mutant Asn56Ala in complexes with sodium and chloride ions
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYoshida, H. / 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
DepositionMar 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,07515
Polymers98,1152
Non-polymers1,96013
Water13,745763
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0558
Polymers49,0581
Non-polymers9987
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-23 kcal/mol
Surface area17450 Å2
MethodPISA
2
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0207
Polymers49,0581
Non-polymers9626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-11 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.119, 109.065, 95.017
Angle α, β, γ (deg.)90.000, 98.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein Uncharacterized protein


Mass: 49057.516 Da / Num. of mol.: 2 / Fragment: UNP residues 1-431 / Mutation: N56A
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 5 types, 776 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 763 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: Tacsimate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→19.64 Å / Num. obs: 80576 / % possible obs: 96 % / Redundancy: 3.58 % / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.08 / Χ2: 0.97 / Net I/σ(I): 6.6 / Num. measured all: 290996 / Scaling rejects: 2183
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsΧ2Diffraction-ID% possible all
1.8-1.863.540.5141.81.17193.3
1.86-1.943.530.45821.15193.8
1.94-2.033.510.3932.41.16194.3
2.03-2.133.490.3292.71.09194.9
2.13-2.273.480.263.21.01195.2
2.27-2.443.530.20440.96196.6
2.44-2.693.620.1525.20.9196.9
2.69-3.073.720.0957.80.82197.8
3.07-3.873.710.0515.10.75198.4
3.87-19.643.70.04119.30.73199.1

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Processing

Software
NameVersionClassification
CrystalCleardata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
d*TREKdata scaling
CrystalCleardata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T1F

5t1f


Resolution: 1.8→19.64 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.062 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.155
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 4016 5 %RANDOM
Rwork0.2092 ---
obs0.212 76559 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.36 Å2 / Biso mean: 32.891 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.8→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 123 763 7546
Biso mean--27.57 37.67 -
Num. residues----862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0196965
X-RAY DIFFRACTIONr_bond_other_d00.026496
X-RAY DIFFRACTIONr_angle_refined_deg0.8581.9639471
X-RAY DIFFRACTIONr_angle_other_deg0.527314947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3795862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33323.77305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.612151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8021541
X-RAY DIFFRACTIONr_chiral_restr0.0560.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217902
X-RAY DIFFRACTIONr_gen_planes_other00.021619
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 277 -
Rwork0.355 5448 -
all-5725 -
obs--93.53 %

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