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

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Basic information

Entry
Database: PDB / ID: 8iqa
TitleCrystal structure of Pyruvic Oxime Dioxygenase (POD) from Alcaligenes faecalis deleted N-terminal 18 residues
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 / NICKEL (II) ION / Aldolase
Function and homology information
Biological speciesAlcaligenes faecalis subsp. faecalis NBRC 13111 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 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 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,0378
Polymers107,8024
Non-polymers2354
Water12,286682
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12330 Å2
ΔGint-122 kcal/mol
Surface area31760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.22, 135.045, 138.04
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26950.498 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-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% (w/v) PEG 3350, 8%(v/v) tacsimate

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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 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→96.53 Å / Num. obs: 95150 / % possible obs: 94 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 10.7
Reflection shellResolution: 1.55→1.68 Å / Rmerge(I) obs: 0.953 / Num. unique obs: 4756

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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: 1.551→22.68 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.114 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.119 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 4866 -RANDOM
Rwork0.1907 ---
obs0.1918 95105 71 %-
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.5434 Å20 Å20 Å2
2---0.7574 Å20 Å2
3----1.7861 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.551→22.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6916 0 4 682 7602
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017141HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.939788HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2296SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1233HARMONIC5
X-RAY DIFFRACTIONt_it7141HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion990SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7084SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion14.69
LS refinement shellResolution: 1.551→1.63 Å
RfactorNum. reflection% reflection
Rfree0.2568 104 -
Rwork0.2571 --
obs--9.86 %
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)
10.2948-0.24650.08330.53790.0180.38570.0153-0.06650.0687-0.06650.00670.00410.06870.0041-0.0220.017-0.0132-0.0101-0.0115-0.0175-0.036913.7425-10.1578-41.1451
21.40990.1335-0.21380.2595-0.0510.4766-0.05820.05250.05520.0525-0.02070.04970.05520.04970.0789-0.00320.0050.0282-0.01850.0267-0.008816.2142-16.5586-11.355
30.31470.182-0.08480.26010.05250.2671-0.01490.0291-0.07780.02910.0182-0.0166-0.0778-0.0166-0.00340.04720.00720.0073-0.0248-0.0059-0.045118.335413.5343-4.8916
40.5397-0.0578-0.01480.38590.00120.7166-0.0412-0.0662-0.1437-0.06620.00680.0113-0.14370.01130.03440.061-0.0142-0.0148-0.0425-0.0022-0.055715.363820.1329-34.7896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A29 - 257
2X-RAY DIFFRACTION1{ A|* }A300
3X-RAY DIFFRACTION2{ B|* }B28 - 259
4X-RAY DIFFRACTION2{ B|* }B300
5X-RAY DIFFRACTION3{ C|* }C27 - 260
6X-RAY DIFFRACTION3{ C|* }C300
7X-RAY DIFFRACTION4{ D|* }D29 - 258
8X-RAY DIFFRACTION4{ D|* }D300

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