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- PDB-7cup: Structure of 2,5-dihydroxypridine Dioxygenase from Pseudomonas pu... -

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Basic information

Entry
Database: PDB / ID: 7cup
TitleStructure of 2,5-dihydroxypridine Dioxygenase from Pseudomonas putida KT2440
Components2,5-dihydroxypyridine 5,6-dioxygenase
KeywordsOXIDOREDUCTASE / non-heme dioxygenase
Function / homology2,5-dihydroxypyridine 5,6-dioxygenase / 2,5-dihydroxypyridine 5,6-dioxygenase activity / : / nicotinate catabolic process / metal ion binding / : / 2,5-dihydroxypyridine 5,6-dioxygenase
Function and homology information
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, G.Q. / Tang, H.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2020
Title: 2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypridine and product N-formylmaleamic acid
Authors: Liu, G.Q. / Tang, H.Z.
History
DepositionAug 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,5-dihydroxypyridine 5,6-dioxygenase
B: 2,5-dihydroxypyridine 5,6-dioxygenase
C: 2,5-dihydroxypyridine 5,6-dioxygenase
D: 2,5-dihydroxypyridine 5,6-dioxygenase
E: 2,5-dihydroxypyridine 5,6-dioxygenase
F: 2,5-dihydroxypyridine 5,6-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,87512
Polymers243,5406
Non-polymers3356
Water27,2211511
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20810 Å2
ΔGint-141 kcal/mol
Surface area67780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.961, 143.750, 118.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
2,5-dihydroxypyridine 5,6-dioxygenase / 2 / 5-DHP dioxygenase / Nicotinate degradation protein X


Mass: 40589.938 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Strain: KT2440 / Gene: nicX, PP_3945 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q88FY1, 2,5-dihydroxypyridine 5,6-dioxygenase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1511 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350 0.2 M Succinic acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 142933 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 1 / Net I/σ(I): 25
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 6863 / CC1/2: 0.972

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CNT

7cnt


Resolution: 2→47.41 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.602 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 2013 1.4 %RANDOM
Rwork0.1712 ---
obs0.1718 139196 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.83 Å2 / Biso mean: 27.746 Å2 / Biso min: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16328 0 6 1511 17845
Biso mean--40.29 38.04 -
Num. residues----2086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01316718
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715272
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.64722714
X-RAY DIFFRACTIONr_angle_other_deg1.3861.57435396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.54552080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99722.039912
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.569152718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.72415120
X-RAY DIFFRACTIONr_chiral_restr0.0780.22134
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023550
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.289 128 -
Rwork0.254 8852 -
obs--83.9 %

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