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- PDB-4i58: Cyclohexylamine Oxidase from Brevibacterium oxydans IH-35A -

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Basic information

Entry
Database: PDB / ID: 4i58
TitleCyclohexylamine Oxidase from Brevibacterium oxydans IH-35A
ComponentsCyclohexylamine Oxidase
KeywordsOXIDOREDUCTASE / flavoprotein / monoamine oxidase / cyclohexylamine oxidase / biocatalysis
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Cyclohexylamine Oxidase
Similarity search - Component
Biological speciesBrevibacterium oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMirza, I.A. / Berghuis, A.M.
CitationJournal: Plos One / Year: 2013
Title: Structural Analysis of a Novel Cyclohexylamine Oxidase from Brevibacterium oxydans IH-35A.
Authors: Mirza, I.A. / Burk, D.L. / Xiong, B. / Iwaki, H. / Hasegawa, Y. / Grosse, S. / Lau, P.C. / Berghuis, A.M.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclohexylamine Oxidase
B: Cyclohexylamine Oxidase
C: Cyclohexylamine Oxidase
D: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,7028
Polymers204,5604
Non-polymers3,1424
Water0
1
A: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9252
Polymers51,1401
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9252
Polymers51,1401
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9252
Polymers51,1401
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cyclohexylamine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9252
Polymers51,1401
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)217.715, 234.588, 90.047
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain AAAA,CCCC, using strict)
NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.7141, -0.7, 0.0034), (0.7, 0.7141, 0.0104), (-0.0097, -0.005, 0.9999)31.3356, -77.5313, -10.6631
3given(0.7013, 0.7128, 0.0105), (-0.7128, 0.7013, -0.0017), (-0.0086, -0.0063, 0.9999)30.789, 77.3039, 11.7031
4given(-0.0043, 1, 0.0007), (-1, -0.0043, -0.0004), (-0.0004, -0.0007, 1)108.8099, 108.6196, 22.503

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Components

#1: Protein
Cyclohexylamine Oxidase /


Mass: 51139.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacterium oxydans (bacteria) / Strain: IH-35A / Gene: chaA / Plasmid: pSD80 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: R4GRV2*PLUS
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM

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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: 2.93 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 30% PEG 8000, 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Details: Mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 46346 / Num. obs: 44399 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.143 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
3-3.110.403192.8
3.11-3.230.295193.3
3.23-3.380.261193.7
3.38-3.560.201194.6
3.56-3.780.16195.2
3.78-4.070.132196.4
4.07-4.480.103196.6
4.48-5.130.089197.5
5.13-6.460.088198.7
6.46-500.083199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.3refinement
PDB_EXTRACT3.11data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GOS

1gos


Resolution: 3→45.8 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 85358.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4323 10.1 %RANDOM
Rwork0.237 ---
obs0.237 42689 91.9 %-
all-46616 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.785 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.92 Å20 Å20 Å2
2---6.29 Å20 Å2
3---10.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13820 0 212 0 14032
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 606 9.7 %
Rwork0.347 5657 -
obs--81.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6fad_xplor.parfad_xplor.top

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