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- PDB-6iwe: Crystal structure of fructosyl peptide oxidase thermally stable mutant -

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Basic information

Entry
Database: PDB / ID: 6iwe
TitleCrystal structure of fructosyl peptide oxidase thermally stable mutant
ComponentsFructosyl peptide oxidase
KeywordsOXIDOREDUCTASE / fructosyl peptide oxidase / thermal mutant
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor / 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
FLAVIN-ADENINE DINUCLEOTIDE / Fructosyl peptide oxidase
Similarity search - Component
Biological speciesPenicillium terrenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.939 Å
AuthorsFuqing, M. / Guangyu, Y.
CitationJournal: To Be Published
Title: crystal structure of fructosyl peptide oxidase thermally stable mutant
Authors: Fuqiang, M. / Guangyu, Y.
History
DepositionDec 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructosyl peptide oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2622
Polymers48,4761
Non-polymers7861
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-12 kcal/mol
Surface area17300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.251, 80.251, 130.347
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Fructosyl peptide oxidase


Mass: 48476.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium terrenum (fungus) / Gene: fpoxE / Production host: Escherichia coli (E. coli)
References: UniProt: Q765A9, Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M potassium phosphate dibasic, 20%(w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.97→47.52 Å / Num. obs: 36666 / % possible obs: 100 % / Redundancy: 5.06 % / Net I/σ(I): 16
Reflection shellResolution: 1.97→2 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.939→47.54 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 1760 4.8 %
Rwork0.208 --
obs0.21 34963 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.939→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 53 60 3475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083507
X-RAY DIFFRACTIONf_angle_d0.9494762
X-RAY DIFFRACTIONf_dihedral_angle_d5.3012039
X-RAY DIFFRACTIONf_chiral_restr0.054507
X-RAY DIFFRACTIONf_plane_restr0.007605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9394-1.99180.31871330.27512639X-RAY DIFFRACTION100
1.9918-2.05050.31141480.26452653X-RAY DIFFRACTION100
2.0505-2.11660.30681370.24672633X-RAY DIFFRACTION100
2.1166-2.19230.28781410.22672630X-RAY DIFFRACTION100
2.1923-2.28010.27621560.2292638X-RAY DIFFRACTION100
2.2801-2.38380.26151370.22842657X-RAY DIFFRACTION100
2.3838-2.50950.27811390.23642670X-RAY DIFFRACTION100
2.5095-2.66670.30291370.2422659X-RAY DIFFRACTION100
2.6667-2.87260.27061080.22822706X-RAY DIFFRACTION100
2.8726-3.16160.27761450.23612663X-RAY DIFFRACTION100
3.1616-3.6190.25691160.20132733X-RAY DIFFRACTION100
3.619-4.55890.19251290.16072740X-RAY DIFFRACTION100
4.5589-47.55470.20591340.17992885X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -23.3763 Å / Origin y: 33.4423 Å / Origin z: 19.8214 Å
111213212223313233
T-0.1943 Å2-0.0607 Å20.0007 Å2-0.3425 Å2-0.0433 Å2--0.1203 Å2
L0.2921 °2-0.0831 °2-0.0566 °2-0.0371 °20.0275 °2--0.0427 °2
S0.1739 Å °0.2342 Å °-0.0487 Å °-0.1236 Å °-0.0637 Å °-0.0698 Å °0.0094 Å °-0.0574 Å °0.1614 Å °
Refinement TLS groupSelection details: all

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