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- PDB-2gbx: Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas y... -

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Basic information

Entry
Database: PDB / ID: 2gbx
TitleCrystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1 Bound to Biphenyl
Components(Biphenyl 2,3-Dioxygenase ...) x 2
KeywordsOXIDOREDUCTASE / RIESKE OXYGENASE / NON HEME IRON / DIOXYGENASE
Function / homology
Function and homology information


3-phenylpropionate catabolic process / catabolic process / dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding / metal ion binding
Similarity search - Function
Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 ...Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Nuclear Transport Factor 2; Chain: A, - #50 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BIPHENYL / : / FE2/S2 (INORGANIC) CLUSTER / Biphenyl/naphthalene dioxygenase alpha subunit / Biphenyl/naphthalene dioxygenase beta subunit
Similarity search - Component
Biological speciesSphingobium yanoikuyae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFerraro, D.J. / Brown, E.N. / Yu, C. / Parales, R.E. / Gibson, D.T. / Ramaswamy, S.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1.
Authors: Ferraro, D.J. / Brown, E.N. / Yu, C.L. / Parales, R.E. / Gibson, D.T. / Ramaswamy, S.
History
DepositionMar 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 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 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 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.ptnr2_auth_asym_id / _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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE According to authors, there is no aminoacid sequence database reference available for the protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biphenyl 2,3-Dioxygenase Alpha Subunit
B: Biphenyl 2,3-Dioxygenase Beta Subunit
C: Biphenyl 2,3-Dioxygenase Alpha Subunit
D: Biphenyl 2,3-Dioxygenase Beta Subunit
E: Biphenyl 2,3-Dioxygenase Alpha Subunit
F: Biphenyl 2,3-Dioxygenase Beta Subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,21624
Polymers215,4706
Non-polymers1,74618
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31290 Å2
ΔGint-448 kcal/mol
Surface area59540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.940, 133.940, 219.708
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe alpha-3 beta-3 assembly is the biological assembly, and is fully contained in the assymetric unit.

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Components

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Biphenyl 2,3-Dioxygenase ... , 2 types, 6 molecules ACEBDF

#1: Protein Biphenyl 2,3-Dioxygenase Alpha Subunit


Mass: 51036.898 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium yanoikuyae (bacteria) / Strain: B1 / Gene: bphA1fA2f / Plasmid: pET101D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2TC87
#2: Protein Biphenyl 2,3-Dioxygenase Beta Subunit


Mass: 20786.336 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium yanoikuyae (bacteria) / Plasmid: pET101D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2TC88

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Non-polymers , 5 types, 205 molecules

#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical ChemComp-BNL / BIPHENYL


Mass: 154.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H10
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 277.15 K / pH: 6.8
Details: 20% PEG3350, 1.0 M Sodium Chloride, 0.037M Zinc Chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K, pH 6.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: CRYOGENICALLY-COOLED SI(111) DOUBLE-CRYSTAL SYSTEM
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→19.481 Å / Num. all: 56587 / Num. obs: 56587 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 47.22 Å2
Reflection shellResolution: 2.8→3 Å / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 6.3 / % possible all: 98.7

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Phasing

Phasing MRRfactor: 0.322 / Cor.coef. Fo:Fc: 0.734 / Cor.coef. Io to Ic: 0.736
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
JDirectordata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GBW

2gbw


Resolution: 2.8→19.48 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.863 / SU B: 33.994 / SU ML: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.268 1132 2 %
Rwork0.237 --
obs0.238 56587 100 %
all-56587 -
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14987 0 60 187 15234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02115512
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210662
X-RAY DIFFRACTIONr_angle_refined_deg0.6711.9321038
X-RAY DIFFRACTIONr_angle_other_deg0.698325605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.16251868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.10923.2825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.618152468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.12415135
X-RAY DIFFRACTIONr_chiral_restr0.0420.22134
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0217626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023538
X-RAY DIFFRACTIONr_nbd_refined0.1320.23325
X-RAY DIFFRACTIONr_nbd_other0.1450.211678
X-RAY DIFFRACTIONr_nbtor_refined0.1690.27584
X-RAY DIFFRACTIONr_nbtor_other0.0750.27898
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0760.2383
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0020.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1110.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0470.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1131.511958
X-RAY DIFFRACTIONr_mcbond_other0.0051.53793
X-RAY DIFFRACTIONr_mcangle_it0.117214831
X-RAY DIFFRACTIONr_scbond_it0.01137606
X-RAY DIFFRACTIONr_scangle_it0.0144.56191
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å
RfactorNum. reflection% reflection
Rfree0.342 80 -
Rwork0.316 3936 -
obs--100 %

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