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- PDB-3gzy: Crystal Structure of the Biphenyl Dioxygenase from Comamonas test... -

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Basic information

Entry
Database: PDB / ID: 3gzy
TitleCrystal Structure of the Biphenyl Dioxygenase from Comamonas testosteroni Sp. Strain B-356
Components(Biphenyl dioxygenase subunit ...) x 2
KeywordsOXIDOREDUCTASE / DIOXYGENASE / RIESKIE / NON-HEME IRON / Aromatic hydrocarbons catabolism / Iron / Iron-sulfur / Metal-binding / NAD
Function / homology
Function and homology information


biphenyl 2,3-dioxygenase / biphenyl 2,3-dioxygenase activity / : / 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] iron-sulphur domain / Rieske [2Fe-2S] 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 dioxygenase subunit alpha / Biphenyl dioxygenase subunit beta
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsKumar, P. / Colbert, C.L. / Bolin, J.T.
CitationJournal: Plos One / Year: 2013
Title: Structural Characterization of Pandoraea pnomenusa B-356 Biphenyl Dioxygenase Reveals Features of Potent Polychlorinated Biphenyl-Degrading Enzymes
Authors: Colbert, C.L. / Agar, N.Y. / Kumar, P. / Chakko, M.N. / Sinha, S.C. / Powlowski, J.B. / Eltis, L.D. / Bolin, J.T.
History
DepositionApr 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 6, 2013Group: Database references
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.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.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: Biphenyl dioxygenase subunit alpha
B: Biphenyl dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7625
Polymers73,3352
Non-polymers4273
Water10,449580
1
A: Biphenyl dioxygenase subunit alpha
B: Biphenyl dioxygenase subunit beta
hetero molecules

A: Biphenyl dioxygenase subunit alpha
B: Biphenyl dioxygenase subunit beta
hetero molecules

A: Biphenyl dioxygenase subunit alpha
B: Biphenyl dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,28615
Polymers220,0056
Non-polymers1,2819
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area32390 Å2
ΔGint-194 kcal/mol
Surface area57550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.233, 136.233, 106.237
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-208-

HOH

21B-248-

HOH

31B-351-

HOH

41B-419-

HOH

51B-580-

HOH

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Components

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Biphenyl dioxygenase subunit ... , 2 types, 2 molecules AB

#1: Protein Biphenyl dioxygenase subunit alpha / Biphenyl 2 / 3-dioxygenase


Mass: 51751.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Gene: bphA / Production host: Escherichia coli (E. coli) / References: UniProt: Q46372, biphenyl 2,3-dioxygenase
#2: Protein Biphenyl dioxygenase subunit beta / Biphenyl 2 / 3-dioxygenase


Mass: 21583.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Gene: bphE / Production host: Escherichia coli (E. coli) / References: UniProt: Q46373, biphenyl 2,3-dioxygenase

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Non-polymers , 4 types, 583 molecules

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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20-15% PEG 4000, 100mM MES, 10-15% 2-PROPANOL, SODIUM CHLORIDE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. all: 91600 / Num. obs: 91600 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 13
Reflection shellResolution: 1.62→1.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.194 / % possible all: 99.4

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Processing

Software
NameClassification
HKL-2000data collection
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NDO

1ndo


Resolution: 1.62→39.33 Å / Num. parameters: 22850 / Num. restraintsaints: 21403 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
all0.118 91600 --
obs-91600 93.5 %-
Rfree---RANDOM
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5520.45
Refinement stepCycle: LAST / Resolution: 1.62→39.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5023 0 17 580 5620
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.064
X-RAY DIFFRACTIONs_approx_iso_adps0

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