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- PDB-4mjw: Crystal Structure of Choline Oxidase in Complex with the Reaction... -

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Basic information

Entry
Database: PDB / ID: 4mjw
TitleCrystal Structure of Choline Oxidase in Complex with the Reaction Product Glycine Betaine
ComponentsCholine oxidase
KeywordsOXIDOREDUCTASE / Reaction Product / Glycine Betaine / Choline / Oxidase / FAD Binding / Glucose-Methanol-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 / TRIMETHYL GLYCINE / FLAVIN-ADENINE DINUCLEOTIDE / Choline oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, Y.-F. / Salvi, F. / Gadda, G. / Weber, I.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of choline oxidase in complex with the reaction product glycine betaine.
Authors: Salvi, F. / Wang, Y.F. / Weber, I.T. / Gadda, G.
History
DepositionSep 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Sep 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_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Choline oxidase
B: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,09112
Polymers119,7982
Non-polymers2,29410
Water13,223734
1
A: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0466
Polymers59,8991
Non-polymers1,1475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Choline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0466
Polymers59,8991
Non-polymers1,1475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.350, 87.350, 353.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Choline oxidase /


Mass: 59898.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: codA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7X2H8, choline oxidase

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Non-polymers , 5 types, 744 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-BET / TRIMETHYL GLYCINE / Trimethylglycine


Mass: 118.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12NO2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 734 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: mixing 1 uL of choline oxidase (6.6 mg/mL) with 1 uL of reservoir solution containing 0.1 M magnesium acetate, pH 6.0, 50 mM calcium chloride, 2.5% v/v glycerol, and 10% w/v PEG 6000 ...Details: mixing 1 uL of choline oxidase (6.6 mg/mL) with 1 uL of reservoir solution containing 0.1 M magnesium acetate, pH 6.0, 50 mM calcium chloride, 2.5% v/v glycerol, and 10% w/v PEG 6000 (reservoir 500 uL), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.95→43.35 Å / Num. all: 97679 / Num. obs: 92704 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3 / Num. unique all: 8823 / % possible all: 89.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JBV

2jbv


Resolution: 1.95→43.35 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.609 / SU ML: 0.068 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.114 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.18106 4869 5 %RANDOM
Rwork0.15099 ---
obs0.1525 92704 96.94 %-
all-97679 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.531 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8212 0 154 734 9100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198614
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3351.96711738
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62551073
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3623.478414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.669151335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.551580
X-RAY DIFFRACTIONr_chiral_restr0.170.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0216726
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_it1.411.2444268
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8681.855329
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1541.5594346
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.85511.64613878
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 307 -
Rwork0.201 5991 -
obs-5991 86.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.26520.0986-0.18780.3499-0.07420.64740.0124-0.01260.01560.00890.00410.0069-0.03520.0092-0.01650.041-0.00040.01360.02580.00410.0106-37.906-2.392-13.122
20.31930.0982-0.0420.2875-0.09090.47980.00780.0170.0060.00460.01970.0204-0.0054-0.0667-0.02750.02970.00860.01090.01530.00690.0061-40.935-7.165-52.42
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 601
2X-RAY DIFFRACTION2B1 - 601

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