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- PDB-7da9: Structure of 6-hydroxy-3-succinoyl-pyridine 3-monooxygenase (HspB... -

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Basic information

Entry
Database: PDB / ID: 7da9
TitleStructure of 6-hydroxy-3-succinoyl-pyridine 3-monooxygenase (HspB) from Pseudomonas putida S16
Components6-hydroxy-3-succinoylpyridine 3-monooxygenase HspB
KeywordsOXIDOREDUCTASE / monooxygenase
Function / homology
Function and homology information


6-hydroxy-3-succinoylpyridine 3-monooxygenase / nicotine catabolic process / alkaloid metabolic process / FAD binding / monooxygenase activity
Similarity search - Function
: / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
6-hydroxy-3-succinoylpyridine 3-monooxygenase HspB
Similarity search - Component
Biological speciesPseudomonas putida S16 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.108 Å
AuthorsLiu, G.Q. / Liu, G.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structure of 6-hydroxy-3-succinoyl-pyridine 3-monooxygenase (HspB) from Pseudomonas putida S16
Authors: Liu, G.Q. / Liu, G.Q.
History
DepositionOct 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-hydroxy-3-succinoylpyridine 3-monooxygenase HspB
B: 6-hydroxy-3-succinoylpyridine 3-monooxygenase HspB


Theoretical massNumber of molelcules
Total (without water)88,0462
Polymers88,0462
Non-polymers00
Water8,701483
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-1 kcal/mol
Surface area31050 Å2
Unit cell
Length a, b, c (Å)67.417, 83.779, 79.560
Angle α, β, γ (deg.)90.000, 114.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 6-hydroxy-3-succinoylpyridine 3-monooxygenase HspB / 6-hydroxy-3-succinoylpyridine hydroxylase / HSP hydroxylase


Mass: 44023.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida S16 (bacteria) / Strain: S16 / Gene: hspB, PPS_4061 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: F8G0M4, 6-hydroxy-3-succinoylpyridine 3-monooxygenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 25% PEG4000, 0.1 mol/L Bis-Tris pH 8.0, 0.2 mol/L MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 45977 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.993 / Net I/σ(I): 21.13
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 2290 / CC1/2: 0.708

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AIN

6ain


Resolution: 2.108→30.563 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 2004 4.39 %
Rwork0.1809 43622 -
obs0.1833 45626 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.17 Å2 / Biso mean: 28.7832 Å2 / Biso min: 10.04 Å2
Refinement stepCycle: final / Resolution: 2.108→30.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 0 483 6591
Biso mean---33.35 -
Num. residues----776
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1081-2.16090.27891320.2007293095
2.1609-2.21930.27631420.2005309997
2.2193-2.28450.38411400.2752304197
2.2845-2.35830.29811420.1986311499
2.3583-2.44250.31351440.1916314499
2.4425-2.54030.27691450.187312499
2.5403-2.65580.30011390.195312899
2.6558-2.79570.2361420.18310599
2.7957-2.97080.21231450.1789315699
2.9708-3.19990.22691420.1786318699
3.1999-3.52150.24781470.1722311899
3.5215-4.03010.22721460.158312898
4.0301-5.07370.15821460.1537315199
5.0737-30.5630.21261520.1902319898
Refinement TLS params.Method: refined / Origin x: 11.269 Å / Origin y: -14.2177 Å / Origin z: -11.4467 Å
111213212223313233
T0.1232 Å20.0146 Å20.0064 Å2-0.1167 Å20.0144 Å2--0.1769 Å2
L0.3309 °20.0269 °2-0.0577 °2-0.5734 °20.0434 °2--1.1131 °2
S-0.0302 Å °-0.0843 Å °-0.0131 Å °0.0715 Å °-0.0172 Å °0.0487 Å °0.0697 Å °-0.0405 Å °0.0311 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 392
2X-RAY DIFFRACTION1allB5 - 392
3X-RAY DIFFRACTION1allW1 - 483

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