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- PDB-1uli: Biphenyl dioxygenase (BphA1A2) derived from Rhodococcus sp. strai... -

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Basic information

Entry
Database: PDB / ID: 1uli
TitleBiphenyl dioxygenase (BphA1A2) derived from Rhodococcus sp. strain RHA1
Components
  • biphenyl dioxygenase large subunit
  • biphenyl dioxygenase small subunit
KeywordsOXIDOREDUCTASE / Alpha3 Beta3 hetero hexamer
Function / homology
Function and homology information


biphenyl 2,3-dioxygenase / biphenyl 2,3-dioxygenase activity / 3-phenylpropionate catabolic process / catabolic process / 2 iron, 2 sulfur cluster binding / iron 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
: / FE2/S2 (INORGANIC) CLUSTER / Biphenyl 2,3-dioxygenase subunit alpha / Biphenyl 2,3-dioxygenase subunit beta
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFurusawa, Y. / Nagarajan, V. / Masai, E. / Tanokura, M. / Fukuda, M. / Senda, T.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of the Terminal Oxygenase Component of Biphenyl Dioxygenase Derived from Rhodococcus sp. Strain RHA1
Authors: Furusawa, Y. / Nagarajan, V. / Tanokura, M. / Masai, E. / Fukuda, M. / Senda, T.
#1: Journal: Protein Pept.Lett. / Year: 2003
Title: Crystallization Of The Terminal Oxygenase Component Of Biphenyl Dioxygenase Derived From Rhodococcus Sp. Strain Rha1
Authors: Nagarajan, V. / Sakurai, N. / Kubota, M. / Nonaka, T. / Nagumo, H. / Takeda, H. / Nishizaki, T. / Masai, E. / Fukuda, M. / Senda, T.
History
DepositionSep 12, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: biphenyl dioxygenase large subunit
B: biphenyl dioxygenase small subunit
C: biphenyl dioxygenase large subunit
D: biphenyl dioxygenase small subunit
E: biphenyl dioxygenase large subunit
F: biphenyl dioxygenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,83413
Polymers221,0836
Non-polymers7517
Water13,511750
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31840 Å2
ΔGint-186 kcal/mol
Surface area55070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.741, 137.741, 237.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein biphenyl dioxygenase large subunit


Mass: 51644.566 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): IAM1399 / References: UniProt: Q53122, biphenyl 2,3-dioxygenase
#2: Protein biphenyl dioxygenase small subunit


Mass: 22049.848 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): IAM1399 / References: UniProt: Q53123, biphenyl 2,3-dioxygenase
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 750 / 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: 2.62 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2002
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 153515 / Num. obs: 153515 / % possible obs: 85.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 8.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.5 / Num. unique all: 12618 / Rsym value: 0.292 / % possible all: 49

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.07 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.994 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20067 5714 5 %RANDOM
Rwork0.16727 ---
all0.16893 110357 --
obs0.16893 109044 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.018 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14579 0 16 750 15345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02114976
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213083
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.92720281
X-RAY DIFFRACTIONr_angle_other_deg0.81330327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77451797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.22073
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216950
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023333
X-RAY DIFFRACTIONr_nbd_refined0.1860.22798
X-RAY DIFFRACTIONr_nbd_other0.2430.215582
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.28384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2861
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.090.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0820.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5591.58968
X-RAY DIFFRACTIONr_mcangle_it1.061214388
X-RAY DIFFRACTIONr_scbond_it1.56236008
X-RAY DIFFRACTIONr_scangle_it2.6274.55887
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.237 427
Rwork0.167 7743

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