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- PDB-7e7h: Crystal Structure of a pseudooxynicotine amine oxidase Pnao from ... -

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Basic information

Entry
Database: PDB / ID: 7e7h
TitleCrystal Structure of a pseudooxynicotine amine oxidase Pnao from Pseudomonas putida S16
ComponentsAmino_oxidase domain-containing protein
KeywordsOXIDOREDUCTASE / amine oxidase
Function / homologyFlavin amine oxidase / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / Amino_oxidase domain-containing protein
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTang, H.Z.
CitationJournal: To Be Published
Title: Crystal Structure of a pseudooxynicotine amine oxidase Pnao from Pseudomonas putida S16
Authors: Tang, H.Z.
History
DepositionFeb 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: 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: Amino_oxidase domain-containing protein
B: Amino_oxidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0027
Polymers104,9802
Non-polymers2,0225
Water8,683482
1
A: Amino_oxidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7265
Polymers52,4901
Non-polymers1,2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-11 kcal/mol
Surface area16520 Å2
MethodPISA
2
B: Amino_oxidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2762
Polymers52,4901
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-11 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.657, 89.709, 157.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Amino_oxidase domain-containing protein


Mass: 52489.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: PU99_05505 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3D0T5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate, 25 % PEG 3350, BIS-TRIS ph 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 51082 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 30.24 Å2 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.065 / Net I/σ(I): 18.5
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 2538 / Rpim(I) all: 0.223

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C71

6c71


Resolution: 2.2→34.83 Å / SU ML: 0.2026 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5172
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2216 1908 3.93 %
Rwork0.1654 46581 -
obs0.1676 48489 94.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6774 0 136 482 7392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00757076
X-RAY DIFFRACTIONf_angle_d0.90479610
X-RAY DIFFRACTIONf_chiral_restr0.05221048
X-RAY DIFFRACTIONf_plane_restr0.00471216
X-RAY DIFFRACTIONf_dihedral_angle_d18.87022538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.27981240.19373012X-RAY DIFFRACTION87.04
2.25-2.310.2641300.19253049X-RAY DIFFRACTION88.43
2.31-2.380.22421240.1873126X-RAY DIFFRACTION90.71
2.38-2.460.23851270.17253182X-RAY DIFFRACTION91.81
2.46-2.550.26371320.18393179X-RAY DIFFRACTION92.1
2.55-2.650.22151320.17543270X-RAY DIFFRACTION93.95
2.65-2.770.23591370.17673319X-RAY DIFFRACTION95.79
2.77-2.920.23531390.17153410X-RAY DIFFRACTION97.21
2.92-3.10.24581390.16323403X-RAY DIFFRACTION98.64
3.1-3.340.20931430.1593499X-RAY DIFFRACTION99.62
3.34-3.670.20481450.15763521X-RAY DIFFRACTION99.78
3.67-4.20.19571450.14583512X-RAY DIFFRACTION99.81
4.2-5.290.18851450.14823545X-RAY DIFFRACTION99.27
5.29-34.830.24491460.18253554X-RAY DIFFRACTION95.21

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