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- PDB-7de0: Crystal structure of FtmOx1 Y224F mutation -

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Basic information

Entry
Database: PDB / ID: 7de0
TitleCrystal structure of FtmOx1 Y224F mutation
ComponentsFtmOx1
KeywordsALLERGEN / FtmOX1 / endoperoxidation / a-Ketoglutarate / mononuclear non-haem iron enzyme / catalytic mechanism
Function / homology:
Function and homology information
Biological speciesAspergillus fumigatus AF210 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, F. / Gao, Y.Q. / Gan, J.H. / Cao, C.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21807105, 91753119, 21977110 and 21778065 China
National Natural Science Foundation of China (NSFC)2017YFE0108200 and 2016YFA0502302 China
CitationJournal: Catalysis Science And Technology / Year: 2023
Title: Structure-based Insights into Mechanism of Endoperoxidase FtmOx1 Catalyzed Reactions
Authors: Wang, F. / Gao, Y.Q. / Wang, C.X. / Lan, W.X. / Gan, J.H. / Cao, C.Y.
History
DepositionOct 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: FtmOx1
A: FtmOx1
C: FtmOx1
D: FtmOx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,2588
Polymers135,0344
Non-polymers2234
Water84747
1
B: FtmOx1
C: FtmOx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6294
Polymers67,5172
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-49 kcal/mol
Surface area23170 Å2
MethodPISA
2
A: FtmOx1
D: FtmOx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6294
Polymers67,5172
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-49 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.436, 136.740, 180.628
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
FtmOx1


Mass: 33758.598 Da / Num. of mol.: 4 / Mutation: Y224F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus AF210 (mold) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 100 mM Bicine, 300mM MgCl2, PEG 2000

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 45093 / % possible obs: 98.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 31.84 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.04 / Rrim(I) all: 0.13 / Χ2: 0.982 / Net I/σ(I): 6.3 / Num. measured all: 356990
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.494.30.42941990.3540.2120.4830.79794.6
2.49-2.5950.42144150.4490.1940.4670.83498.2
2.59-2.75.70.41244660.6090.1780.4520.85498.9
2.7-2.8560.36644600.720.1540.3990.92598.9
2.85-3.027.40.32244820.8740.120.3450.97699.4
3.02-3.268.20.2645040.9440.0910.2771.05899.5
3.26-3.588.90.18745110.9820.0620.1971.10299.6
3.58-4.110.10.1345790.9920.0410.1361.11899.8
4.1-5.1611.50.09646400.9960.0280.11.04499.8
5.16-3011.40.08148370.9950.0240.0850.8699.5

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL2Mapphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y5T

4y5t


Resolution: 2.4→29.728 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 25.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 1969 5.02 %
Rwork0.2155 37236 -
obs0.2179 39205 86.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.54 Å2 / Biso mean: 30.0744 Å2 / Biso min: 13.83 Å2
Refinement stepCycle: final / Resolution: 2.4→29.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8935 0 4 47 8986
Biso mean--36.77 21.65 -
Num. residues----1134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079153
X-RAY DIFFRACTIONf_angle_d0.86612465
X-RAY DIFFRACTIONf_chiral_restr0.0481401
X-RAY DIFFRACTIONf_plane_restr0.0061646
X-RAY DIFFRACTIONf_dihedral_angle_d14.9345591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.460.304580.2623110437
2.46-2.52650.3154760.2686146148
2.5265-2.60080.31641050.2887188464
2.6008-2.68470.33121390.2845246781
2.6847-2.78060.32241270.2679274991
2.7806-2.89180.30471770.2639288597
2.8918-3.02330.3321440.2526305099
3.0233-3.18260.28051540.2423299599
3.1826-3.38170.29231670.2319303199
3.3817-3.64240.27641580.20483047100
3.6424-4.00810.2581550.19453076100
4.0081-4.58630.19741800.17653083100
4.5863-5.77130.24671720.18433120100
5.7713-29.7280.21911570.18913284100
Refinement TLS params.Method: refined / Origin x: -6.2634 Å / Origin y: 3.2059 Å / Origin z: -19.1317 Å
111213212223313233
T0.1615 Å2-0.0198 Å20.0039 Å2-0.215 Å2-0.0147 Å2--0.1912 Å2
L0.4824 °20.3815 °2-0.3717 °2-0.6926 °2-0.5821 °2--0.7347 °2
S0.0607 Å °-0.0895 Å °-0.02 Å °0.1339 Å °-0.0204 Å °-0.0167 Å °-0.1633 Å °0.0056 Å °-0.0201 Å °
Refinement TLS groupSelection details: all

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