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- PDB-8il8: Crystal structure of Pyruvic Oxime Dioxygenase (POD) from Alcalig... -

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Basic information

Entry
Database: PDB / ID: 8il8
TitleCrystal structure of Pyruvic Oxime Dioxygenase (POD) from Alcaligenes faecalis
ComponentsAldolaseFructose-bisphosphate aldolase
KeywordsOXIDOREDUCTASE / class II aldolase-like / dioxygenase / non-heme iron / His-triad
Function / homologyClass II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / : / Aldolase
Function and homology information
Biological speciesAlcaligenes faecalis subsp. faecalis NBRC 13111 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.769 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: To Be Published
Title: Structural and functional analysis of pyruvic oxime dioxygenase, a key enzyme of heterotrophic nitrification
Authors: Tsujino, S. / Yamada, Y. / Senda, M. / Senda, T. / Fujiwara, T.
History
DepositionMar 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,7798
Polymers116,5564
Non-polymers2234
Water12,484693
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-132 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.002, 107.552, 87.794
Angle α, β, γ (deg.)90, 128.07, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Aldolase / Fructose-bisphosphate aldolase / Pyruvic oxime dioxygenase


Mass: 29138.920 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis subsp. faecalis NBRC 13111 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A2N3A3
#2: Chemical
ChemComp-FE2 / FE (II) 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 / Water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 36% (v/v) PEG 400, 0.2M calcium acetate, 0.1M HEPES

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.76→76.44 Å / Num. obs: 55281 / % possible obs: 93.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 8.9
Reflection shellResolution: 1.76→1.9 Å / Rmerge(I) obs: 0.565 / Num. unique obs: 2766

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
REFMAC5.8.0352refinement
Coot0.9.8.3model building
autoPROC1.0.5data processing
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.769→76.44 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.222 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.233 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 2653 -RANDOM
Rwork0.1822 ---
obs0.1836 55281 56.2 %-
Displacement parametersBiso mean: 32.73 Å2
Baniso -1Baniso -2Baniso -3
1-4.2813 Å20 Å26.2908 Å2
2---4.1832 Å20 Å2
3----0.0981 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.769→76.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7116 0 4 693 7813
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097292HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.929954HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2414SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1250HARMONIC5
X-RAY DIFFRACTIONt_it7292HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion980SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6952SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion16.03
LS refinement shellResolution: 1.77→1.84 Å
RfactorNum. reflection% reflection
Rfree0.2981 52 -
Rwork0.2466 --
obs0.249 1106 10.23 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.96270.04650.00210.7123-0.06830.73860.0694-0.0082-0.2036-0.0082-0.0017-0.0377-0.2036-0.0377-0.06780.06980.02040.116-0.1253-0.00810.004820.834421.559523.1555
20.8717-0.2639-0.14170.50760.01740.7697-0.0344-0.18570.055-0.18570.02240.06130.0550.06130.0120.1109-0.01070.1276-0.09540.0111-0.067237.16424.78852.5431
30.77580.19410.04980.9416-0.05850.8331-0.1-0.00560.0898-0.00560.04180.02970.08980.02970.05820.07680.00210.1019-0.1172-0.0298-0.019526.8233-21.55915.9098
40.70870.0217-0.1860.6130.31811.09870.01260.09590.0420.09590.00230.06130.0420.0613-0.01490.0241-0.02560.1365-0.07980.0088-0.006710.6246-4.716136.6085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A29 - 258
2X-RAY DIFFRACTION1{ A|* }A301
3X-RAY DIFFRACTION2{ B|* }B29 - 258
4X-RAY DIFFRACTION2{ B|* }B301
5X-RAY DIFFRACTION3{ C|* }C29 - 258
6X-RAY DIFFRACTION3{ C|* }C301
7X-RAY DIFFRACTION4{ D|* }D29 - 258
8X-RAY DIFFRACTION4{ D|* }D301

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