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- PDB-8ix6: Crystal structure of Pyruvic Oxime Dioxygenase (POD) from Bradyrh... -

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Basic information

Entry
Database: PDB / ID: 8ix6
TitleCrystal structure of Pyruvic Oxime Dioxygenase (POD) from Bradyrhizobium sp. WSM3983
ComponentsAldolase
KeywordsOXIDOREDUCTASE / class II aldolase-like / dioxygenase / non-heme iron / His-triad
Function / homologyNICKEL (II) ION
Function and homology information
Biological speciesBradyrhizobium sp. WSM3983 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.47 Å
AuthorsTsujino, S. / Yamada, Y. / Fujiwara, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)21K12220 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17K00517 Japan
CitationJournal: J.Bacteriol. / Year: 2025
Title: Structural characterization of pyruvic oxime dioxygenase, a key enzyme in heterotrophic nitrification.
Authors: Tsujino, S. / Yamada, Y. / Senda, M. / Nakamura, A. / Senda, T. / Fujiwara, T.
History
DepositionMar 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8495
Polymers29,5021
Non-polymers3474
Water37821
1
A: Aldolase
hetero molecules

A: Aldolase
hetero molecules

A: Aldolase
hetero molecules

A: Aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,39720
Polymers118,0104
Non-polymers1,38816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
Buried area12590 Å2
ΔGint-267 kcal/mol
Surface area29730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.896, 153.896, 153.896
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Space group name HallI423
Symmetry operation#1: x,y,z
#2: x,-z,y
#3: x,z,-y
#4: z,y,-x
#5: -z,y,x
#6: -y,x,z
#7: y,-x,z
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y,x,-z
#20: -y,-x,-z
#21: z,-y,x
#22: -z,-y,-x
#23: -x,z,y
#24: -x,-z,-y
#25: x+1/2,y+1/2,z+1/2
#26: x+1/2,-z+1/2,y+1/2
#27: x+1/2,z+1/2,-y+1/2
#28: z+1/2,y+1/2,-x+1/2
#29: -z+1/2,y+1/2,x+1/2
#30: -y+1/2,x+1/2,z+1/2
#31: y+1/2,-x+1/2,z+1/2
#32: z+1/2,x+1/2,y+1/2
#33: y+1/2,z+1/2,x+1/2
#34: -y+1/2,-z+1/2,x+1/2
#35: z+1/2,-x+1/2,-y+1/2
#36: -y+1/2,z+1/2,-x+1/2
#37: -z+1/2,-x+1/2,y+1/2
#38: -z+1/2,x+1/2,-y+1/2
#39: y+1/2,-z+1/2,-x+1/2
#40: x+1/2,-y+1/2,-z+1/2
#41: -x+1/2,y+1/2,-z+1/2
#42: -x+1/2,-y+1/2,z+1/2
#43: y+1/2,x+1/2,-z+1/2
#44: -y+1/2,-x+1/2,-z+1/2
#45: z+1/2,-y+1/2,x+1/2
#46: -z+1/2,-y+1/2,-x+1/2
#47: -x+1/2,z+1/2,y+1/2
#48: -x+1/2,-z+1/2,-y+1/2

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Components

#1: Protein Aldolase


Mass: 29502.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium sp. WSM3983 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.56M ammonium sulfate, 25% (v/v) glycerol

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 2.7 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7 Å / Relative weight: 1
ReflectionResolution: 2.47→76.95 Å / Num. obs: 11546 / % possible obs: 100 % / Redundancy: 38.1 % / Biso Wilson estimate: 60.18 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 43.9
Reflection shellResolution: 2.47→2.51 Å / Rmerge(I) obs: 1.766 / Num. unique obs: 569

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
CRANK2phasing
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.47→76.95 Å / SU ML: 0.2418 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.2428
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2577 575 5 %
Rwork0.2299 10927 -
obs0.2314 11502 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.13 Å2
Refinement stepCycle: LAST / Resolution: 2.47→76.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 16 21 1721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211740
X-RAY DIFFRACTIONf_angle_d0.51422380
X-RAY DIFFRACTIONf_chiral_restr0.039265
X-RAY DIFFRACTIONf_plane_restr0.0041306
X-RAY DIFFRACTIONf_dihedral_angle_d3.566240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.720.36231260.28652694X-RAY DIFFRACTION99.89
2.72-3.110.29741330.30252687X-RAY DIFFRACTION99.86
3.11-3.920.29311470.24692710X-RAY DIFFRACTION99.3
3.92-76.950.22621690.19932836X-RAY DIFFRACTION99.44

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