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- PDB-6l6j: Structure of 6-hydroxypseudooxynicotine (6-HPON) amine oxidase (H... -

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Basic information

Entry
Database: PDB / ID: 6l6j
TitleStructure of 6-hydroxypseudooxynicotine (6-HPON) amine oxidase (HisD) from Pseudomonas geniculata N1
ComponentsOxidored_FMN domain-containing protein
KeywordsOXIDOREDUCTASE / amine oxidase
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
Similarity search - Function
NAD(P)-binding Rossmann-like domain / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FAD/NAD(P)-binding domain superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / CITRATE ANION / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / Oxidored_FMN domain-containing protein
Similarity search - Component
Biological species[Pseudomonas] geniculata N1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLiu, G.Q. / Tang, H.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Appl.Environ.Microbiol. / Year: 2020
Title: Structure of 6-hydroxypseudooxynicotine (6-HPON) amine oxidase (HisD) from Pseudomonas geniculata N1
Authors: Liu, G.Q. / Tang, H.Z.
History
DepositionOct 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Oxidored_FMN domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4488
Polymers73,7351
Non-polymers1,7127
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-23 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.110, 212.902, 79.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-704-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Oxidored_FMN domain-containing protein


Mass: 73735.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Pseudomonas] geniculata N1 (bacteria) / Gene: W7K_00670 / Production host: Pseudomonas putida KT2440 (bacteria) / References: UniProt: A0A0L8AFM7

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Non-polymers , 6 types, 116 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.3 Å3/Da / Density % sol: 62.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.5 M Ammonium sulfate 0.1 M Sodium citrate dihydrate pH 5.6 1.0 M Lithium sulfate monohydrate

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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: Jan 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 29678 / % possible obs: 98.8 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.055 / Rrim(I) all: 0.174 / Χ2: 1.015 / Net I/σ(I): 4.8 / Num. measured all: 276129
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.698.20.60127480.9220.2080.6380.8892.7
2.69-2.88.10.53328650.9370.1870.5660.87796
2.8-2.9390.4529350.9550.1530.4760.90199.2
2.93-3.089.70.34829600.9770.1150.3680.937100
3.08-3.289.90.25329870.9850.0830.2670.991100
3.28-3.539.70.18629640.990.0610.1971.096100
3.53-3.889.30.13730150.9930.0450.1441.19399.8
3.88-4.4510.20.10930050.9960.0340.1141.245100
4.45-5.69.20.09130280.9960.030.0961.13399.9
5.6-509.50.0731710.9970.0240.0740.82999.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K30

3k30


Resolution: 2.6→39.97 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.917 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.382 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 1479 4.9 %RANDOM
Rwork0.1703 ---
obs0.172 28917 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.65 Å2 / Biso mean: 34.277 Å2 / Biso min: 14.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0 Å2
2--0.08 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 2.6→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5157 0 94 109 5360
Biso mean--42.39 32.13 -
Num. residues----669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135367
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174898
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.6577317
X-RAY DIFFRACTIONr_angle_other_deg1.3651.58311304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40220.598301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.75415838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8761554
X-RAY DIFFRACTIONr_chiral_restr0.0710.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021173
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 118 -
Rwork0.217 2035 -
all-2153 -
obs--97.33 %

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