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- PDB-7ylo: Conversion of indole-3-acetic acid into indole-3-aldehyde in bact... -

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Basic information

Entry
Database: PDB / ID: 7ylo
TitleConversion of indole-3-acetic acid into indole-3-aldehyde in bacteria Metabolic network of tryptophan around the indole-3-aldehyde formation
ComponentsDyp-type peroxidase
KeywordsOXIDOREDUCTASE / peroxidase / LyP / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesLimosilactobacillus fermentum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.83 Å
AuthorsCheng, J. / Luo, Y. / Zhu, J. / Tan, R. / Wang, N. / Lebedev, A.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2024
Title: Molecular Insights into the One-Carbon Loss Oxidation of Indole-3-acetic Acid
Authors: Cheng, J. / Wang, N. / Yu, L. / Luo, Y. / Liu, A.K. / Tang, S. / Xu, J.Y. / Wang, Y.S. / Zhu, J. / Lebedev, A. / Tian, C.L. / Tan, R.X.
History
DepositionJul 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 22, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dyp-type peroxidase
B: Dyp-type peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8374
Polymers72,6042
Non-polymers1,2332
Water4,179232
1
A: Dyp-type peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9192
Polymers36,3021
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dyp-type peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9192
Polymers36,3021
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.179, 135.179, 83.979
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: TYR / End label comp-ID: TYR / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 3 - 313 / Label seq-ID: 3 - 313

Dom-ID
1
2

NCS ensembles : (Details: Global NCS restraints between domains: 1 2)
NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-1, -2.0E-5, -1.9E-5), (-2.0E-5, 1, -6.3E-5), (1.9E-5, -6.3E-5, -1)135.179565, 0.00376, 62.98473

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Components

#1: Protein Dyp-type peroxidase / Iron-dependent peroxidase / Peroxidase


Mass: 36302.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus fermentum (bacteria)
Gene: BUW47_03110, C1Y38_03730, DBX48_02645, GC247_08580, GDZ34_00450, GJA14_02385, LACFE_CDS1279
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G9GI91
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1.0 M lithium sulfate, 0.1 M sodium citrate (pH 5.6) and 0.5 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.83→67.59 Å / Num. obs: 36030 / % possible obs: 92.5 % / Redundancy: 17.6 % / CC1/2: 0.98 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.04 / Rrim(I) all: 0.168 / Χ2: 0.97 / Net I/σ(I): 14.9
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 12.3 % / Rmerge(I) obs: 2.304 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 687 / CC1/2: 0.372 / Rpim(I) all: 0.655 / Rrim(I) all: 2.41 / Χ2: 0.77 / % possible all: 58.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.83→67.589 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.184 / SU B: 2.794 / SU ML: 0.078 / Average fsc free: 0 / Average fsc work: 0 / Cross valid method: NONE / ESU R: 0.31 / ESU R Free: 0.225
Details: Hydrogens have been added in their riding positions. The model represents an ordered domain of a partially disordered crystal. Reflections L=2N+1 were severely affected by crystal disorder ...Details: Hydrogens have been added in their riding positions. The model represents an ordered domain of a partially disordered crystal. Reflections L=2N+1 were severely affected by crystal disorder and could not be measured. Reflections L=2N were not affected by crystal disorder and were used for structure solution and refinement. Scaling and merging was done in point group 6 2 2, c=42.0A. Refinement was conducted against 50% complete P 3 2 1 data set, c=84A, see associated manuscript for details.
RfactorNum. reflection% reflection
Rfree0.2376 1800 4.996 %
Rwork0.2018 34230 -
all0.204 --
obs-36030 46.201 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.268 Å2
Baniso -1Baniso -2Baniso -3
1-0.458 Å20.229 Å20 Å2
2--0.458 Å2-0 Å2
3----1.486 Å2
Refinement stepCycle: LAST / Resolution: 1.83→67.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4984 0 86 232 5302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125202
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164462
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6797094
X-RAY DIFFRACTIONr_angle_other_deg0.5691.57610396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6255620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.5131032
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35610782
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.99410280
X-RAY DIFFRACTIONr_chiral_restr0.0720.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026066
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021080
X-RAY DIFFRACTIONr_nbd_refined0.1950.2990
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.24156
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22518
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22522
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2201
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.215
X-RAY DIFFRACTIONr_nbd_other0.1710.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.210
X-RAY DIFFRACTIONr_mcbond_it1.8642.2622486
X-RAY DIFFRACTIONr_mcbond_other1.8632.2622486
X-RAY DIFFRACTIONr_mcangle_it2.6813.3833104
X-RAY DIFFRACTIONr_mcangle_other2.6813.3833105
X-RAY DIFFRACTIONr_scbond_it2.3722.552716
X-RAY DIFFRACTIONr_scbond_other2.3672.5492714
X-RAY DIFFRACTIONr_scangle_it3.6533.7353990
X-RAY DIFFRACTIONr_scangle_other3.6483.7353990
X-RAY DIFFRACTIONr_lrange_it4.81128.5285748
X-RAY DIFFRACTIONr_lrange_other4.79528.5145742
Refine LS restraints NCS

Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Rms dev Biso : 0.10112 Å2 / Rms dev position: 0.00437 Å / Weight Biso : 0.5 / Weight position: 0.05

Dom-ID
1
2
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 all% reflection obs (%)WRfactor Rwork
1.83-1.8780.411740.31615870.32568929.19670.3
1.878-1.9290.4511120.4217690.421555933.8370.415
1.929-1.9850.3061290.26420420.266544539.87140.239
1.985-2.0460.2991090.22424290.227525548.29690.196
2.046-2.1130.3011310.23223730.236513048.81090.196
2.113-2.1870.2621240.18623000.19492349.23830.159
2.187-2.270.3731110.31722130.32479548.46720.297
2.27-2.3620.2871200.24721580.249458249.71630.206
2.362-2.4670.2681100.17520980.179442749.87580.152
2.467-2.5870.305750.16420070.168421049.45370.142
2.587-2.7270.2171210.1718870.173404049.7030.148
2.727-2.8920.188750.17218390.172383249.94780.156
2.892-3.0920.212800.20216930.202356549.73350.188
3.092-3.3390.238850.20815860.21335449.82110.2
3.339-3.6560.217700.18114780.182312149.59950.177
3.656-4.0860.167810.16913350.169279350.69820.173
4.086-4.7160.141630.13411810.135248450.08050.142
4.716-5.7690.221650.1739880.176212049.66980.182
5.769-8.1290.23500.2017850.203166550.15020.208
8.129-67.5890.168150.2094820.20799350.05040.222

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