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- PDB-2zi8: Crystal structure of the HsaC extradiol dioxygenase from M. tuber... -

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Basic information

Entry
Database: PDB / ID: 2zi8
TitleCrystal structure of the HsaC extradiol dioxygenase from M. tuberculosis in complex with 3,4-dihydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione (DHSA)
ComponentsPROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC
KeywordsOXIDOREDUCTASE / DHSA / HsaC / extradiol dioxygenase / Mycobacterium tuberculosis / Aromatic hydrocarbons catabolism / Iron
Function / homology
Function and homology information


3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione 4,5-dioxygenase / 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione 4,5-dioxygenase activity / : / response to cholesterol / cholesterol catabolic process / cholesterol metabolic process / lipid catabolic process / ferrous iron binding / iron ion binding
Similarity search - Function
: / Dihydroxybiphenyl dioxygenase BphC D1 / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / : / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain ...: / Dihydroxybiphenyl dioxygenase BphC D1 / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / : / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / Chem-SDT / Iron-dependent extradiol dioxygenase / Iron-dependent extradiol dioxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsD'Angelo, I. / Yam, K.C. / Eltis, L.D. / Strynadka, N.
CitationJournal: Plos Pathog. / Year: 2009
Title: Studies of a ring-cleaving dioxygenase illuminate the role of cholesterol metabolism in the pathogenesis of Mycobacterium tuberculosis.
Authors: Yam, K.C. / D'Angelo, I. / Kalscheuer, R. / Zhu, H. / Wang, J.X. / Snieckus, V. / Ly, L.H. / Converse, P.J. / Jacobs, W.R. / Strynadka, N. / Eltis, L.D.
History
DepositionFeb 13, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 8, 2020Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_distant_solvent_atoms ...database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3Nov 1, 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_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC
B: PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0016
Polymers67,2572
Non-polymers7444
Water8,719484
1
A: PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC
B: PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC
hetero molecules

A: PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC
B: PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC
hetero molecules

A: PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC
B: PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC
hetero molecules

A: PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC
B: PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,00424
Polymers269,0268
Non-polymers2,97816
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Unit cell
Length a, b, c (Å)124.318, 124.318, 106.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC / EXTRADIOL DIOXYGENASE / 23OHBP OXYGENASE / 2 / 3-DIHYDROXYBIPHENYL DIOXYGENASE / 2 / 3- ...EXTRADIOL DIOXYGENASE / 23OHBP OXYGENASE / 2 / 3-DIHYDROXYBIPHENYL DIOXYGENASE / 2 / 3-DIHYDROXYBIPHENYL 1 / 2- DIOXYGENASE / DHBD / Extradiol ring-cleavage dioxygenase


Mass: 33628.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Plasmid: pT7HC1 / Production host: Escherichia coli (E. coli) / Strain (production host): GJ1158
References: UniProt: P96850, UniProt: P9WNW7*PLUS, biphenyl-2,3-diol 1,2-dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SDT / 3,4-dihydroxy-9,10-secoandrosta-1(10),2,4-triene-9,17-dione / 3,4-dhsa


Mass: 316.391 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12-15% PEG 3350, 0.2M ammonium tartrate, 25% ethylene glycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2007 / Details: MC
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 56012 / Num. obs: 55996 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 26
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 6.1 / Num. unique all: 6156 / Rsym value: 0.389 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HAN

1han


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.884 / SU B: 6.703 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.224 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 2156 5 %RANDOM
Rwork0.19388 ---
obs0.19738 40622 99.94 %-
all-40622 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.477 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2---0.83 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 48 484 5236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0214869
X-RAY DIFFRACTIONr_angle_refined_deg2.4471.9696601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.5795601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52622.134239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.17315787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9661558
X-RAY DIFFRACTIONr_chiral_restr0.2370.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023808
X-RAY DIFFRACTIONr_nbd_refined0.2680.22176
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2469
X-RAY DIFFRACTIONr_metal_ion_refined0.2740.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.230
X-RAY DIFFRACTIONr_mcbond_it1.3541.53077
X-RAY DIFFRACTIONr_mcangle_it2.08224741
X-RAY DIFFRACTIONr_scbond_it3.37532074
X-RAY DIFFRACTIONr_scangle_it4.8264.51857
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 166 -
Rwork0.296 2919 -
obs--99.87 %

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