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- PDB-6lqc: Crystal structure of Cyclohexylamine Oxidase from Erythrobacterac... -

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Basic information

Entry
Database: PDB / ID: 6lqc
TitleCrystal structure of Cyclohexylamine Oxidase from Erythrobacteraceae bacterium
ComponentsCyclohexylamine Oxidase
KeywordsOXIDOREDUCTASE / Cyclohexylamine Oxidase
Function / homology
Function and homology information


Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE
Similarity search - Component
Biological speciesErythrobacteraceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsHuang, Z.D.
CitationJournal: J.Org.Chem. / Year: 2020
Title: Asymmetric Synthesis of a Key Dextromethorphan Intermediate and Its Analogues Enabled by a New Cyclohexylamine Oxidase: Enzyme Discovery, Reaction Development, and Mechanistic Insight.
Authors: Wu, X. / Huang, Z. / Wang, Z. / Li, Z. / Wang, J. / Lin, J. / Chen, F.
History
DepositionJan 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 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

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Assembly

Deposited unit
A: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7762
Polymers48,9911
Non-polymers7861
Water9,692538
1
A: Cyclohexylamine Oxidase
hetero molecules

A: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5534
Polymers97,9822
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5410 Å2
ΔGint-27 kcal/mol
Surface area30270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.591, 82.591, 175.279
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-671-

HOH

21A-795-

HOH

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Components

#1: Protein Cyclohexylamine Oxidase


Mass: 48990.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erythrobacteraceae bacterium (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10 % PEG 8000,100 mM Potassium phosphate monobasic/ Sodium phosphate dibasic pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 50354 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 31.06 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.042 / Net I/σ(I): 41
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 24.1 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2452 / Rpim(I) all: 0.254 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I59

4i59


Resolution: 1.88→24.3 Å / SU ML: 0.1769 / Cross valid method: FREE R-VALUE / σ(F): 0.61 / Phase error: 19.8862
RfactorNum. reflection% reflection
Rfree0.1895 1851 3.96 %
Rwork0.172 --
obs0.1727 46754 92.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.7 Å2
Refinement stepCycle: LAST / Resolution: 1.88→24.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 53 538 4025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01553598
X-RAY DIFFRACTIONf_angle_d1.66014910
X-RAY DIFFRACTIONf_chiral_restr0.0962527
X-RAY DIFFRACTIONf_plane_restr0.0113638
X-RAY DIFFRACTIONf_dihedral_angle_d16.97291263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.28811230.23823086X-RAY DIFFRACTION84.71
1.93-1.990.22031300.22173063X-RAY DIFFRACTION83.94
1.99-2.050.22771290.21193130X-RAY DIFFRACTION85.99
2.05-2.120.26091340.20983288X-RAY DIFFRACTION89.39
2.12-2.210.20251320.2013245X-RAY DIFFRACTION89.01
2.21-2.310.21061410.18913517X-RAY DIFFRACTION95.33
2.31-2.430.21751470.19263441X-RAY DIFFRACTION93.15
2.43-2.580.24741420.19353515X-RAY DIFFRACTION95.46
2.58-2.780.23021470.19543574X-RAY DIFFRACTION96.57
2.78-3.060.20871530.19193666X-RAY DIFFRACTION98.2
3.06-3.50.18781500.16443681X-RAY DIFFRACTION98.51
3.5-4.410.12911580.13673780X-RAY DIFFRACTION99.19
4.41-24.30.17721650.15393917X-RAY DIFFRACTION97.87

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