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

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Basic information

Entry
Database: PDB / ID: 7cnt
TitleStructure of 2,5-dihydroxypridine Dioxygenase from Pseudomonas putida KT2440 in complex with product N-formylmaleamic acid formed via in crystallo reaction with 2,5-dihydroxypridine
Components2,5-dihydroxypyridine 5,6-dioxygenase
KeywordsOXIDOREDUCTASE / dihydroxypridine / formylmaleamic acid
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 / SAD / Resolution: 2.28 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 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)247,25112
Polymers246,9166
Non-polymers3356
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20710 Å2
ΔGint-142 kcal/mol
Surface area68290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.885, 125.916, 144.129
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 41152.680 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-FE2 / FE (II) 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.: 241 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Succnic acid PH7 20%PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 98134 / % possible obs: 99.2 % / Redundancy: 6 % / Rrim(I) all: 0.101 / Net I/σ(I): 8.7
Reflection shellResolution: 2.28→2.4 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 14230 / Rrim(I) all: 0.711

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.28→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.387 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 4901 5 %RANDOM
Rwork0.2106 ---
obs0.2135 93165 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 173.03 Å2 / Biso mean: 67.306 Å2 / Biso min: 32.03 Å2
Baniso -1Baniso -2Baniso -3
1--3.2 Å20 Å2-0 Å2
2---3.51 Å20 Å2
3---6.71 Å2
Refinement stepCycle: final / Resolution: 2.28→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16338 0 6 241 16585
Biso mean--97.21 55.06 -
Num. residues----2088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01916758
X-RAY DIFFRACTIONr_bond_other_d00.0215712
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9722772
X-RAY DIFFRACTIONr_angle_other_deg3.635336149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75452088
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5123.854794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.101152524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.14215121
X-RAY DIFFRACTIONr_chiral_restr0.090.22487
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02119145
X-RAY DIFFRACTIONr_gen_planes_other0.010.023852
LS refinement shellResolution: 2.28→2.339 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 346 -
Rwork0.319 6806 -
all-7152 -
obs--99.31 %

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