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- PDB-8i6i: Crystal structure of cyclohexylamine oxidase from Acinetobacter s... -

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Basic information

Entry
Database: PDB / ID: 8i6i
TitleCrystal structure of cyclohexylamine oxidase from Acinetobacter sp. YT-02
ComponentsAmine oxidase
KeywordsFLAVOPROTEIN / Cyclohexylamine oxidase
Function / homology: / Flavin amine oxidase / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / FLAVIN-ADENINE DINUCLEOTIDE / Amine oxidase
Function and homology information
Biological speciesAcinetobacter sp. YT-02 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsHan, Z. / Yan, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of cyclohexylamine oxidase from Acinetobacter sp. YT-02
Authors: Han, Z.
History
DepositionJan 28, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amine oxidase
C: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6544
Polymers97,0822
Non-polymers1,5712
Water16,430912
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-28 kcal/mol
Surface area30180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.686, 129.372, 167.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-652-

HOH

21A-946-

HOH

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Components

#1: Protein Amine oxidase / Cyclohexylamine oxidase


Mass: 48541.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cyclohexylamine oxidase is a member of amine oxidases that can catalyze the conversion of cyclohexylamine to cyclohexanone and hydrogen peroxide, which is involved in the primary and key ...Details: Cyclohexylamine oxidase is a member of amine oxidases that can catalyze the conversion of cyclohexylamine to cyclohexanone and hydrogen peroxide, which is involved in the primary and key step in the microbial degradation of cyclohexylamine.
Source: (gene. exp.) Acinetobacter sp. YT-02 (bacteria) / Gene: CF596_10820 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2A5PFR1
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 912 / Source method: isolated from a natural source / Formula: H2O
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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M sodium citrate (pH 5.5) and 20% PEG1000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.49→45.91 Å / Num. obs: 173006 / % possible obs: 89.52 % / Redundancy: 2 % / Rrim(I) all: 0.0217 / Net I/σ(I): 21
Reflection shellResolution: 1.49→1.543 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 12624 / Rrim(I) all: 0.351

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→45.91 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.089 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18855 8644 5 %RANDOM
Rwork0.16236 ---
obs0.16364 165335 89.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.411 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.49→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6844 0 106 913 7863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0137124
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176414
X-RAY DIFFRACTIONr_angle_refined_deg1.811.6329714
X-RAY DIFFRACTIONr_angle_other_deg1.5751.57114832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7255894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39722.123358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.392151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5341546
X-RAY DIFFRACTIONr_chiral_restr0.0960.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.028120
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021548
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6581.9073582
X-RAY DIFFRACTIONr_mcbond_other1.6571.9063581
X-RAY DIFFRACTIONr_mcangle_it2.3282.8634474
X-RAY DIFFRACTIONr_mcangle_other2.3282.8634475
X-RAY DIFFRACTIONr_scbond_it3.2672.2583542
X-RAY DIFFRACTIONr_scbond_other3.2682.2593539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8713.2545241
X-RAY DIFFRACTIONr_long_range_B_refined7.20824.0198463
X-RAY DIFFRACTIONr_long_range_B_other6.79223.2158214
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.524 Å
RfactorNum. reflection% reflection
Rfree0.372 429 -
Rwork0.343 8404 -
obs--61.86 %

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