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- PDB-7cn3: 2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypri... -

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Basic information

Entry
Database: PDB / ID: 7cn3
Title2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypridine and product N-formylmaleamic acid
Components2,5-dihydroxypyridine 5,6-dioxygenase
KeywordsOXIDOREDUCTASE / oxidoreductase complex
Function / homology2,5-dihydroxypyridine 5,6-dioxygenase / 2,5-dihydroxypyridine 5,6-dioxygenase activity / : / metal ion binding / Chem-D6O / : / 5-oxidanyl-1H-pyridin-2-one / TRIETHYLENE GLYCOL / 2,5-dihydroxypyridine 5,6-dioxygenase
Function and homology information
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionJul 30, 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

Downloads & links

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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)245,40228
Polymers243,5406
Non-polymers1,86322
Water16,898938
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23080 Å2
ΔGint-120 kcal/mol
Surface area66800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.673, 145.510, 118.976
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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

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Non-polymers , 6 types, 960 molecules

#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-D6O / (~{Z})-4-formamido-4-oxidanylidene-but-2-enoic acid


Mass: 143.097 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-G6C / 5-oxidanyl-1H-pyridin-2-one


Mass: 111.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 938 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density meas: 47.17 Mg/m3 / Density % sol: 47.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Succinic acid pH7.0 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 113279 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 1 / Net I/σ(I): 24.4
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 5529 / CC1/2: 1

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KOH

6koh
PDB Unreleased entry


Resolution: 2.2→27.59 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 5561 4.99 %
Rwork0.1832 105797 -
obs0.186 111358 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.69 Å2 / Biso mean: 35.8463 Å2 / Biso min: 14.95 Å2
Refinement stepCycle: final / Resolution: 2.2→27.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16360 0 110 938 17408
Biso mean--49.83 38.86 -
Num. residues----2090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2250.31251690.2415347499
2.225-2.25120.3161740.2295346699
2.2512-2.27860.28541720.2218347199
2.2786-2.30740.27481660.2207352099
2.3074-2.33780.29052190.22273485100
2.3378-2.36980.28861860.22413445100
2.3698-2.40360.32561970.23463488100
2.4036-2.43950.30041880.2293517100
2.4395-2.47760.28731850.2131349299
2.4776-2.51820.28041990.21183468100
2.5182-2.56160.29091960.21713485100
2.5616-2.60810.29651590.20853547100
2.6081-2.65820.25811860.20843485100
2.6582-2.71240.31121700.20913558100
2.7124-2.77140.28431720.20143528100
2.7714-2.83580.25451960.20753514100
2.8358-2.90660.28252150.20493476100
2.9066-2.98510.28271820.20243542100
2.9851-3.07280.25661690.20223535100
3.0728-3.17190.28372010.21593519100
3.1719-3.28510.25811710.20573547100
3.2851-3.41640.23441900.19143546100
3.4164-3.57150.25581910.17883519100
3.5715-3.75940.21461550.16813583100
3.7594-3.99430.20371920.16453552100
3.9943-4.30160.17362050.14443559100
4.3016-4.73260.17651870.13393594100
4.7326-5.41290.16821720.13883619100
5.4129-6.80270.20211920.16343628100
6.8027-27.590.19862050.1521363596
Refinement TLS params.Method: refined / Origin x: 30.4446 Å / Origin y: 33.405 Å / Origin z: 89.3904 Å
111213212223313233
T0.1836 Å20.0036 Å20.0318 Å2-0.1377 Å2-0.0061 Å2--0.1871 Å2
L0.6528 °2-0.0114 °20.385 °2-0.3099 °20.0084 °2--0.7529 °2
S0.005 Å °0.072 Å °-0.029 Å °-0.0654 Å °-0.0086 Å °0.0033 Å °0.0758 Å °0.0331 Å °0.0048 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 2001
2X-RAY DIFFRACTION1allB2 - 2001
3X-RAY DIFFRACTION1allC2 - 2001
4X-RAY DIFFRACTION1allD2 - 2001
5X-RAY DIFFRACTION1allE2 - 2001
6X-RAY DIFFRACTION1allF2 - 2001
7X-RAY DIFFRACTION1allW1 - 938
8X-RAY DIFFRACTION1allW939 - 940
9X-RAY DIFFRACTION1allS1 - 10

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