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- PDB-1eg9: NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE. -

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Basic information

Entry
Database: PDB / ID: 1eg9
TitleNAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE.
Components(PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ...) x 2
KeywordsOXIDOREDUCTASE / NON-HEME IRON DIOXYGENASE / ENZYME-SUBSTRATE COMPLEX
Function / homology
Function and homology information


naphthalene 1,2-dioxygenase / naphthalene 1,2-dioxygenase activity / 3-phenylpropionate catabolic process / dioxygenase activity / 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 / INDOLE / Naphthalene 1,2-dioxygenase system, large oxygenase component / Naphthalene 1,2-dioxygenase system, small oxygenase component
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsCarredano, E. / Karlsson, A. / Kauppi, B. / Choudhury, D. / Parales, R.E. / Parales, J.V. / Lee, K. / Gibson, D.T. / Eklund, H. / Ramaswamy, S.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding.
Authors: Carredano, E. / Karlsson, A. / Kauppi, B. / Choudhury, D. / Parales, R.E. / Parales, J.V. / Lee, K. / Gibson, D.T. / Eklund, H. / Ramaswamy, S.
History
DepositionFeb 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: 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 / pdbx_struct_special_symmetry / 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_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_label_atom_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_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_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: PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT)
B: PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2708
Polymers72,6332
Non-polymers6376
Water11,025612
1
A: PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT)
B: PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT)
hetero molecules

A: PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT)
B: PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT)
hetero molecules

A: PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT)
B: PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,81124
Polymers217,9006
Non-polymers1,91118
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area32900 Å2
ΔGint-286 kcal/mol
Surface area60930 Å2
MethodPISA
2
A: PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT)
B: PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT)
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)439,62348
Polymers435,80112
Non-polymers3,82236
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)140.169, 140.169, 209.248
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-878-

HOH

21B-889-

HOH

DetailsTHE ACTIVE ENZYME IS A ALPHA3BETA3 HEXAMER GENERATED BY THE THREEFOLD.

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Components

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PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ... , 2 types, 2 molecules AB

#1: Protein PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT)


Mass: 49664.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: PDTG14 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A110, naphthalene 1,2-dioxygenase
#2: Protein PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT)


Mass: 22969.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: PDTG14 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A112, naphthalene 1,2-dioxygenase

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Non-polymers , 5 types, 618 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FE / FE (III) ION


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


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#6: Chemical ChemComp-IND / INDOLE


Mass: 117.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growpH: 6
Details: AMMONIUM SULPHATE 2M, MES 0.1M, DIOXANE 2-3%, pH 6.00
Crystal grow
*PLUS
Temperature: 8 ℃ / Method: vapor diffusion
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
32-3 %dioxane1reservoir
450 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 896312 / % possible obs: 99.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.3
Reflection shellResolution: 1.6→20 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.307 / % possible all: 99
Reflection
*PLUS
Num. obs: 102843 / Num. measured all: 896312
Reflection shell
*PLUS
Lowest resolution: 1.63 Å / % possible obs: 99 % / Mean I/σ(I) obs: 3.31

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.6→20 Å
RfactorNum. reflection
Rfree0.22 1516
Rwork0.19 -
obs0.193 102843
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 29 612 5729
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4

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