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- PDB-1ndo: NAPHTHALENE 1,2-DIOXYGENASE -

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Basic information

Entry
Database: PDB / ID: 1ndo
TitleNAPHTHALENE 1,2-DIOXYGENASE
Components(NAPHTHALENE 1,2-DIOXYGENASE) x 2
KeywordsNON-HEME IRON DIOXYGENASE
Function / homology
Function and homology information


naphthalene 1,2-dioxygenase / naphthalene 1,2-dioxygenase activity / 3-phenylpropionate catabolic process / : / 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 / 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 / MIR, MAD / Resolution: 2.25 Å
AuthorsRamaswamy, S. / Kauppi, B. / Carredano, E.
CitationJournal: Structure / Year: 1998
Title: Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase.
Authors: Kauppi, B. / Lee, K. / Carredano, E. / Parales, R.E. / Gibson, D.T. / Eklund, H. / Ramaswamy, S.
History
DepositionJan 11, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 / 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_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_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: NAPHTHALENE 1,2-DIOXYGENASE
B: NAPHTHALENE 1,2-DIOXYGENASE
C: NAPHTHALENE 1,2-DIOXYGENASE
D: NAPHTHALENE 1,2-DIOXYGENASE
E: NAPHTHALENE 1,2-DIOXYGENASE
F: NAPHTHALENE 1,2-DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,59512
Polymers217,9006
Non-polymers6956
Water19,1141061
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30400 Å2
ΔGint-196 kcal/mol
Surface area61330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.000, 174.000, 282.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.789192, 0.2688, 0.552198), (-0.376054, -0.499358, 0.780528), (0.485551, -0.823643, -0.293006)-28.67416, 33.2988, 74.7929
2given(0.793375, -0.370985, 0.482624), (0.273587, -0.49094, -0.82712), (0.543789, 0.788256, -0.288003)-1.31999, 85.95347, 11.55289

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Components

#1: Protein NAPHTHALENE 1,2-DIOXYGENASE /


Mass: 49664.355 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: CHAIN A,C,E AND B,D,F ARE THE LARGE AND THE SMALL SUBUNITS RESPECTIVELY
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: NAHACAD / Plasmid: PDTG141 / Gene (production host): NAHACAD / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / Variant (production host): DE3 / References: UniProt: P0A110, naphthalene 1,2-dioxygenase
#2: Protein NAPHTHALENE 1,2-DIOXYGENASE /


Mass: 22969.088 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: CHAIN A,C,E AND B,D,F ARE THE LARGE AND THE SMALL SUBUNITS RESPECTIVELY
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: NAHACAD / Plasmid: PDTG141 / Gene (production host): NAHACAD / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / Variant (production host): DE3 / References: UniProt: P0A112, naphthalene 1,2-dioxygenase
#3: Chemical ChemComp-FE / FE (III) ION / Iron


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


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1061 / 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: 2.97 Å3/Da / Density % sol: 59 % / Description: INITIAL PHASES WERE FROM A R32 CRYSTAL FORM
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
22.31 Mammonium sulfate1reservoir
30.1 MMES1reservoir
42 %PEG1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 117067 / % possible obs: 95.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.66
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.386 / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 2.2 Å / % possible obs: 96 % / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 97 % / Num. unique obs: 5920 / Rmerge(I) obs: 0.386

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Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR, MAD / Resolution: 2.25→30 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24 -2 %RANDOM
Rwork0.19 ---
obs0.22 122414 79 %-
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1-4 Å2-6.3 Å20 Å2
2--0 Å22.3 Å2
3---0 Å2
Refine analyzeLuzzati d res low obs: 30 Å
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15270 0 15 2040 17325
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.040.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.060.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.73
X-RAY DIFFRACTIONp_mcangle_it3.75
X-RAY DIFFRACTIONp_scbond_it6.56
X-RAY DIFFRACTIONp_scangle_it7.98
X-RAY DIFFRACTIONp_plane_restr0.04
X-RAY DIFFRACTIONp_chiral_restr0.160.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.210.3
X-RAY DIFFRACTIONp_planar_tor9.67
X-RAY DIFFRACTIONp_staggered_tor18.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.620
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Num. reflection obs: 110479 / Rfactor obs: 0.194 / Rfactor Rfree: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS

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