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

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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 / homologyRieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulphur domain superfamily / Rieske [2Fe-2S] iron-sulfur domain profile. / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Ring hydroxylating beta subunit / Ring hydroxylating alpha subunit (catalytic domain) / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site ...Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulphur domain superfamily / Rieske [2Fe-2S] iron-sulfur domain profile. / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Ring hydroxylating beta subunit / Ring hydroxylating alpha subunit (catalytic domain) / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Rieske [2Fe-2S] domain / NTF2-like domain superfamily / naphthalene 1,2-dioxygenase / naphthalene 1,2-dioxygenase activity / aromatic compound catabolic process / 2 iron, 2 sulfur cluster binding / dioxygenase activity / iron ion binding / Naphthalene 1,2-dioxygenase system, large oxygenase component / Naphthalene 1,2-dioxygenase system, small oxygenase component
Function and homology information
Specimen sourcePseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1.6 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 15, 2000 / Release: May 24, 2000
RevisionDateData content typeGroupProviderType
1.0May 24, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Polyers72,6332
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
Polyers217,9006
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 area (Å2)32900
ΔGint (kcal/M)-286
Surface area (Å2)60930
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
Polyers435,80112
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
γ
α
β
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-MH 3 2
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/peptide PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT)


Mass: 49664.355 Da / Num. of mol.: 1 / Source: (gene. exp.) Pseudomonas putida (bacteria) / Genus: Pseudomonas / Plasmid name: PDTG14 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P0A110, naphthalene 1,2-dioxygenase
#2: Protein/peptide PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT)


Mass: 22969.088 Da / Num. of mol.: 1 / Source: (gene. exp.) Pseudomonas putida (bacteria) / Genus: Pseudomonas / Plasmid name: PDTG14 / Genus (production host): Escherichia / 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 / Formula: SO4 / Sulfate
#4: Chemical ChemComp-FE / FE (III) ION


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


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


Mass: 117.148 Da / Num. of mol.: 1 / Formula: C8H7N / Indole
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / Formula: H2O / Water

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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 / Density percent sol: 54.82 %
Crystal growpH: 6
Details: AMMONIUM SULPHATE 2M, MES 0.1M, DIOXANE 2-3%, pH 6.00
Crystal grow
*PLUS
Temp: 8 ℃ / Method: vapor diffusion
Details: drop consists of equal volume of protein and reservoir solutions
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
130 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
32-3 %dioxane1reservoir
450 mMMES1reservoir

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Collection date: Dec 5, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 16.8 Å2 / D resolution high: 1.6 Å / D resolution low: 2 Å / Number obs: 896312 / Rmerge I obs: 0.072 / NetI over sigmaI: 11.3 / Redundancy: 8.8 % / Percent possible obs: 99.9
Reflection shellRmerge I obs: 0.307 / Highest resolution: 1.6 Å / Lowest resolution: 2 Å / Redundancy: 4.9 % / Percent possible all: 99
Reflection
*PLUS
Number obs: 102843 / Number measured all: 896312
Reflection shell
*PLUS
Lowest resolution: 1.63 Å / Percent possible obs: 99 / MeanI over sigI obs: 3.31

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
Least-squares processR factor R free: 0.22 / R factor R work: 0.19 / R factor obs: 0.193 / Highest resolution: 1.6 Å / Lowest resolution: 2 Å / Number reflection R free: 1516 / Number reflection obs: 102843
Refine hist #LASTHighest resolution: 1.6 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 5088 / Nucleic acid: 0 / Ligand: 29 / Solvent: 612 / Total: 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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