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- PDB-3nne: Crystal structure of choline oxidase S101A mutant -

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Basic information

Entry
Database: PDB / ID: 3nne
TitleCrystal structure of choline oxidase S101A mutant
ComponentsCholine oxidase
KeywordsOXIDOREDUCTASE / Oxidase / Flavoprotein / Kinetics / Reductive half-reaction / Choline
Function / homology
Function and homology information


choline oxidase / choline:oxygen 1-oxidoreductase activity / glycine betaine biosynthetic process from choline / flavin adenine dinucleotide binding
Similarity search - Function
Arc Repressor Mutant - #110 / Glucose Oxidase; domain 2 / Glucose Oxidase, domain 2 / Cholesterol Oxidase; domain 2 - #40 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Arc Repressor Mutant / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase ...Arc Repressor Mutant - #110 / Glucose Oxidase; domain 2 / Glucose Oxidase, domain 2 / Cholesterol Oxidase; domain 2 - #40 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Arc Repressor Mutant / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / Choline oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsWang, Y.-F. / Finnegan, S. / Yuan, H. / Orville, A.M. / Weber, I.T. / Gadda, G.
CitationJournal: Arch.Biochem.Biophys. / Year: 2010
Title: Structural and kinetic studies on the Ser101Ala variant of choline oxidase: Catalysis by compromise.
Authors: Finnegan, S. / Yuan, H. / Wang, Y.F. / Orville, A.M. / Weber, I.T. / Gadda, G.
History
DepositionJun 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choline oxidase
B: Choline oxidase
C: Choline oxidase
D: Choline oxidase
E: Choline oxidase
F: Choline oxidase
G: Choline oxidase
H: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)485,81924
Polymers479,0628
Non-polymers6,75716
Water5,855325
1
A: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7273
Polymers59,8831
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7273
Polymers59,8831
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7273
Polymers59,8831
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7273
Polymers59,8831
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7273
Polymers59,8831
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7273
Polymers59,8831
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7273
Polymers59,8831
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7273
Polymers59,8831
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.258, 346.029, 105.919
Angle α, β, γ (deg.)90.00, 94.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Choline oxidase


Mass: 59882.754 Da / Num. of mol.: 8 / Mutation: S101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: codA / Production host: Escherichia coli (E. coli) / Strain (production host): Jm109 / References: UniProt: Q7X2H8, choline oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 80 mM Nacacodylate and 150 mM Mg-Acetate at pH 6, with 20% v/v PEG6000 and 20% v/v glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. all: 176109 / Num. obs: 159203 / % possible obs: 90.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 14
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.258 / % possible all: 50.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JBV

2jbv


Resolution: 2.47→29.99 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.851 / SU B: 26.159 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.856 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29254 7966 5 %RANDOM
Rwork0.22789 ---
obs0.23117 150964 90.78 %-
all-159203 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0.02 Å2
2---0.13 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.47→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32757 0 456 325 33538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02134262
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.96546764
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09254280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45423.5641664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.816155302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.25315308
X-RAY DIFFRACTIONr_chiral_restr0.1060.25031
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02126850
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6451.521199
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.204234199
X-RAY DIFFRACTIONr_scbond_it1.917313063
X-RAY DIFFRACTIONr_scangle_it3.114.512531
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.468→2.532 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 322 -
Rwork0.309 5296 -
obs--51.11 %
Refinement TLS params.Method: refined / Origin x: 44.2817 Å / Origin y: 1.2056 Å / Origin z: 77.3784 Å
111213212223313233
T0.0155 Å20.0073 Å20.0121 Å2-0.0088 Å20.0046 Å2--0.0139 Å2
L0.0375 °2-0.0012 °20.0069 °2-0.0398 °20.0069 °2--0.0388 °2
S-0.0016 Å °-0.012 Å °-0.0037 Å °-0.016 Å °-0.001 Å °-0.0216 Å °0.0145 Å °0.0107 Å °0.0026 Å °

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