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- PDB-3aff: Crystal structure of the HsaA monooxygenase from M. tuberculosis -

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Basic information

Entry
Database: PDB / ID: 3aff
TitleCrystal structure of the HsaA monooxygenase from M. tuberculosis
ComponentsHydroxylase, putativeHydroxylation
KeywordsOXIDOREDUCTASE / HsaA / cholesterol 3HSA monooxygenase
Function / homology
Function and homology information


3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase / 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / oxidoreductase activity, acting on the CH-CH group of donors / biological process involved in interaction with host / steroid biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / : / cholesterol catabolic process ...3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase / 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / oxidoreductase activity, acting on the CH-CH group of donors / biological process involved in interaction with host / steroid biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / : / cholesterol catabolic process / lipid catabolic process / flavin adenine dinucleotide binding / plasma membrane / cytoplasm
Similarity search - Function
Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily ...Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Flavin-dependent monooxygenase, oxygenase subunit HsaA / Flavin-dependent monooxygenase, oxygenase subunit HsaA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsD'Angelo, I. / Lin, L.Y. / Dresen, C. / Tocheva, E.I. / Strynadka, N. / Eltis, L.D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: A flavin-dependent monooxygenase from Mycobacterium tuberculosis involved in cholesterol catabolism
Authors: Dresen, C. / Lin, L.Y. / D'Angelo, I. / Tocheva, E.I. / Strynadka, N. / Eltis, L.D.
History
DepositionFeb 28, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxylase, putative
B: Hydroxylase, putative


Theoretical massNumber of molelcules
Total (without water)86,3872
Polymers86,3872
Non-polymers00
Water11,205622
1
A: Hydroxylase, putative
B: Hydroxylase, putative

A: Hydroxylase, putative
B: Hydroxylase, putative

A: Hydroxylase, putative
B: Hydroxylase, putative

A: Hydroxylase, putative
B: Hydroxylase, putative


Theoretical massNumber of molelcules
Total (without water)345,5488
Polymers345,5488
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area20710 Å2
ΔGint-122 kcal/mol
Surface area97130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.140, 175.770, 179.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Hydroxylase, putative / Hydroxylation / HsaA / POSSIBLE OXIDOREDUCTASE


Mass: 43193.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P96852, UniProt: P9WJA1*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 15, 2008 / Details: monochromator SI111
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 76266 / Num. obs: 72634 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 26.4

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Processing

Software
NameVersionClassification
CLScustomizeddata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JBS

2jbs


Resolution: 2→19.76 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.548 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23939 3631 5 %RANDOM
Rwork0.19835 ---
all0.2 68987 --
obs0.20041 68987 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.599 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5643 0 0 622 6265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0215859
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9267994
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9275744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09422.832286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10115867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1721555
X-RAY DIFFRACTIONr_chiral_restr0.1450.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024639
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.23002
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23994
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2514
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1761.53753
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78825837
X-RAY DIFFRACTIONr_scbond_it2.99932468
X-RAY DIFFRACTIONr_scangle_it4.6854.52148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 267 -
Rwork0.248 5086 -
obs--100 %

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