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- PDB-1i19: CRYSTAL STRUCTURE OF CHOLESTEROL OXIDASE FROM B.STEROLICUM -

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Basic information

Entry
Database: PDB / ID: 1i19
TitleCRYSTAL STRUCTURE OF CHOLESTEROL OXIDASE FROM B.STEROLICUM
ComponentsCHOLESTEROL OXIDASE
KeywordsOXIDOREDUCTASE / MIX ALPHA BETA / covalent FAD / Flavoenzyme
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor / FAD binding / metal ion binding
Similarity search - Function
Cholesterol oxidase, substrate-binding / Cholesterol oxidase, substrate-binding / L-gulonolactone/D-arabinono-1,4-lactone oxidase / Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidases, C-terminal domain / Cytokinin dehydrogenase, C-terminal domain superfamily / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Vanillyl-alcohol Oxidase; Chain A, domain 3 ...Cholesterol oxidase, substrate-binding / Cholesterol oxidase, substrate-binding / L-gulonolactone/D-arabinono-1,4-lactone oxidase / Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidases, C-terminal domain / Cytokinin dehydrogenase, C-terminal domain superfamily / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / FLAVIN-ADENINE DINUCLEOTIDE / : / Oxidoreductase
Similarity search - Component
Biological speciesBrevibacterium sterolicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsCoulombe, R. / Yue, K.Q. / Ghisla, S. / Vrielink, A.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Oxygen access to the active site of cholesterol oxidase through a narrow channel is gated by an Arg-Glu pair.
Authors: Coulombe, R. / Yue, K.Q. / Ghisla, S. / Vrielink, A.
#1: Journal: J.STRUCT.BIOL. / Year: 1996
Title: Crystallization and Preliminary X-Ray Analysis of Cholesterol Oxidase from Brevibacterium sterolicum Containing Covalently Bound FAD
Authors: Croteau, N. / Vrielink, A.
History
DepositionJan 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHOLESTEROL OXIDASE
B: CHOLESTEROL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,76820
Polymers123,1502
Non-polymers2,61818
Water18,1051005
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A: CHOLESTEROL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6717
Polymers61,5751
Non-polymers1,0966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHOLESTEROL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,09713
Polymers61,5751
Non-polymers1,52212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.440, 124.470, 80.840
Angle α, β, γ (deg.)90.00, 109.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CHOLESTEROL OXIDASE /


Mass: 61575.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COVALENT FAD / Source: (gene. exp.) Brevibacterium sterolicum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SID9, cholesterol oxidase

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Non-polymers , 5 types, 1023 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1005 / 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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 8K, MnSO4, NaCacodylate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Details: Croteau, N., (1996) J.STRUCT.BIOL., 116, 317.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %PEG80001reservoir
275 mM1reservoirMnSO4
3100 mMcacodylate1reservoir
48.5 mg/mlprotein1drop
510 mMHEPES1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 1999
RadiationMonochromator: crystals Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. all: 554010 / Num. obs: 550182 / % possible obs: 94.8 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.6
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.7 / Num. unique all: 7196 / % possible all: 68.4
Reflection
*PLUS
Num. obs: 150202 / Num. measured all: 550182
Reflection shell
*PLUS
% possible obs: 68.4 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.7→36.91 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1351706.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The following atoms have occupancies set to 0.00 or 0.50 because of weak electron density: CG1 and CG2 of VAL 349 chains A and B have occupancy set to 0.00; CG, OD1, ND2 of ASN A 65, all ...Details: The following atoms have occupancies set to 0.00 or 0.50 because of weak electron density: CG1 and CG2 of VAL 349 chains A and B have occupancy set to 0.00; CG, OD1, ND2 of ASN A 65, all atoms of PRO A 330, CG, OD1, OD2 of ASP A 544, CG, OD1, ND2 of ASN B 65, and CG, OD1, OD2 of ASP B 179 have occupancy set to 0.50.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 15006 10 %RANDOM
Rwork0.182 ---
all-150168 --
obs-150168 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.73 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å22.3 Å2
2--0.05 Å20 Å2
3---1.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.7→36.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8415 0 162 1005 9582
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.421.5
X-RAY DIFFRACTIONc_mcangle_it0.752
X-RAY DIFFRACTIONc_scbond_it0.532
X-RAY DIFFRACTIONc_scangle_it0.842.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 2122 10 %
Rwork0.244 19102 -
obs-21224 80.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3FAD_COV.PARAMFAD_COV.TOP
X-RAY DIFFRACTION4EDO.PARAMEDO.TOP
X-RAY DIFFRACTION5IONS.PARAMIONS.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.77
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.264 / % reflection Rfree: 10 % / Rfactor Rwork: 0.244

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