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- PDB-2ig9: Structure of a full-length Homoprotocatechuate 2,3-Dioxygenase fr... -

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Basic information

Entry
Database: PDB / ID: 2ig9
TitleStructure of a full-length Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in a new spacegroup.
ComponentsHomoprotocatechuate 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / oxygenase / extradiol / Fe(II) / homoprotocatechuate
Function / homology
Function and homology information


homoprotocatechuate 2,3-dioxygenase fold / homoprotocatechuate 2,3-dioxygenase domains / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, Mn/Fe-type / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, C-terminal domain superfamily / : / 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 ...homoprotocatechuate 2,3-dioxygenase fold / homoprotocatechuate 2,3-dioxygenase domains / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, Mn/Fe-type / 3,4-dihydroxyphenylacetate 2,3-dioxygenase, C-terminal domain superfamily / : / 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 / Few Secondary Structures / Irregular / Roll / Alpha Beta
Similarity search - Domain/homology
: / Homoprotocatechuate 2,3-dioxygenase
Similarity search - Component
Biological speciesBrevibacterium fuscum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKovaleva, E.G. / Lipscomb, J.D.
CitationJournal: Science / Year: 2007
Title: Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates
Authors: Kovaleva, E.G. / Lipscomb, J.D.
History
DepositionSep 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Homoprotocatechuate 2,3-dioxygenase
B: Homoprotocatechuate 2,3-dioxygenase
C: Homoprotocatechuate 2,3-dioxygenase
D: Homoprotocatechuate 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,44024
Polymers167,0214
Non-polymers1,41820
Water22,4831248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18900 Å2
ΔGint-167 kcal/mol
Surface area43350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.445, 152.802, 99.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1071-

HOH

DetailsA homotetramer composed of chains A-D is the biological unit

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Homoprotocatechuate 2,3-dioxygenase


Mass: 41755.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacterium fuscum (bacteria) / Strain: ATCC 15993 / Gene: hpcd / Plasmid: pYZW204 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q45135, 3,4-dihydroxyphenylacetate 2,3-dioxygenase

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Non-polymers , 5 types, 1268 molecules

#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1248 / 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: 2.29 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG8000, 0.2 M calcium acetate, 0.1 M sodium cacodylate. Prior to freezing in liquid nitrogen, crystals were sequentially transferred into mother liquor solutions containing 5, 10, 15, ...Details: 18% PEG8000, 0.2 M calcium acetate, 0.1 M sodium cacodylate. Prior to freezing in liquid nitrogen, crystals were sequentially transferred into mother liquor solutions containing 5, 10, 15, and then 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.23983 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 24, 2005
RadiationMonochromator: Rosenbaum-Rock sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23983 Å / Relative weight: 1
ReflectionResolution: 1.9→53.15 Å / Num. all: 133141 / Num. obs: 132886 / % possible obs: 99.8 % / Redundancy: 3.18 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2 / Num. unique all: 13150 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
d*TREKdata reduction
d*TREKdata scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F1X

1f1x


Resolution: 1.9→46.08 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.197 / SU ML: 0.118 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Full length enzyme structure solved by molecular replacement using truncated 1F1X (PDB code) structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.23443 6680 5 %RANDOM
Rwork0.1874 ---
obs0.18976 132683 99.67 %-
all-132683 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.337 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11600 0 75 1248 12923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02112171
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.94316547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03651482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88123.434664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19151934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.69315108
X-RAY DIFFRACTIONr_chiral_restr0.1030.21720
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029696
X-RAY DIFFRACTIONr_nbd_refined0.2010.26132
X-RAY DIFFRACTIONr_nbtor_refined0.3050.28300
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.21350
X-RAY DIFFRACTIONr_metal_ion_refined0.1050.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.227
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1650.22
X-RAY DIFFRACTIONr_mcbond_it0.9561.57473
X-RAY DIFFRACTIONr_mcangle_it1.166211767
X-RAY DIFFRACTIONr_scbond_it2.08435335
X-RAY DIFFRACTIONr_scangle_it3.0654.54775
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 501 -
Rwork0.314 9178 -
obs-9178 99.64 %

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