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- PDB-2hml: Crystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant... -

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Basic information

Entry
Database: PDB / ID: 2hml
TitleCrystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Phenanthrene.
Components(Naphthalene 1,2-dioxygenase ...) x 2
KeywordsOXIDOREDUCTASE / Protein / Rieske Oxygenase
Function / homology
Function and homology information


naphthalene 1,2-dioxygenase / naphthalene 1,2-dioxygenase activity / : / 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 / PHENANTHRENE / Naphthalene 1,2-dioxygenase system, large oxygenase component / Naphthalene 1,2-dioxygenase system, small oxygenase component
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 1.8 Å
AuthorsFerraro, D.J. / Okerlund, A.L. / Mowers, J.C. / Ramaswamy, S.
CitationJournal: J.Bacteriol. / Year: 2006
Title: Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase.
Authors: Ferraro, D.J. / Okerlund, A.L. / Mowers, J.C. / Ramaswamy, S.
History
DepositionJul 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 2, 2020Group: Derived calculations / Structure summary / Category: struct_keywords / struct_site
Item: _struct_keywords.text / _struct_site.pdbx_auth_asym_id ..._struct_keywords.text / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Naphthalene 1,2-dioxygenase alpha subunit
B: Naphthalene 1,2-dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,53127
Polymers72,5852
Non-polymers1,94525
Water9,908550
1
A: Naphthalene 1,2-dioxygenase alpha subunit
B: Naphthalene 1,2-dioxygenase beta subunit
hetero molecules

A: Naphthalene 1,2-dioxygenase alpha subunit
B: Naphthalene 1,2-dioxygenase beta subunit
hetero molecules

A: Naphthalene 1,2-dioxygenase alpha subunit
B: Naphthalene 1,2-dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,59281
Polymers217,7566
Non-polymers5,83675
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 area46070 Å2
ΔGint-234 kcal/mol
Surface area57460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)139.865, 139.865, 208.431
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-830-

HOH

21B-761-

HOH

DetailsThe biological assembly is and alpha3 beta3 hexamer. One alpha-beta dimer is in the assymetric unit. The others can be generated by the three-fold axis: y, -x-y, z -x-y, x, z

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Components

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Naphthalene 1,2-dioxygenase ... , 2 types, 2 molecules AB

#1: Protein Naphthalene 1,2-dioxygenase alpha subunit / Naphthalene 1 / 2-dioxygenase ISP alpha


Mass: 49616.312 Da / Num. of mol.: 1 / Mutation: F352V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: doxB / Plasmid: pDTG121 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: P0A111, naphthalene 1,2-dioxygenase
#2: Protein Naphthalene 1,2-dioxygenase beta subunit / Naphthalene 1 / 2-dioxygenase ISP beta


Mass: 22969.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: doxD / Plasmid: pDTG121 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: P0A113, naphthalene 1,2-dioxygenase

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Non-polymers , 6 types, 575 molecules

#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 178.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 279.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.9-2.2 M Ammonium Sulfate, 4-6% Dioxane, 0.1 M MES, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.04021 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Nov 3, 2004
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04021 Å / Relative weight: 1
ReflectionResolution: 1.8→17.97 Å / Num. all: 72381 / Num. obs: 72381 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.66 % / Rmerge(I) obs: 0.108 / Χ2: 0.98 / Net I/σ(I): 9.4 / Scaling rejects: 3407
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.64 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.1 / Num. measured all: 33610 / Num. unique all: 7201 / Χ2: 1.17 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
d*TREK9.2LDzdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
d*TREKdata reduction
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: 1O7H

1o7h


Resolution: 1.8→17.97 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.226 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3651 5 %RANDOM
Rwork0.164 ---
all0.165 72359 --
obs0.165 72359 99.74 %-
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: 15.758 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.18 Å20 Å2
2--0.35 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.8→17.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5069 0 112 550 5731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215291
X-RAY DIFFRACTIONr_bond_other_d0.0020.023611
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.9447128
X-RAY DIFFRACTIONr_angle_other_deg0.87738722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3815636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98624.045267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97215866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1531535
X-RAY DIFFRACTIONr_chiral_restr0.0770.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021118
X-RAY DIFFRACTIONr_nbd_refined0.210.21027
X-RAY DIFFRACTIONr_nbd_other0.2020.23955
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22519
X-RAY DIFFRACTIONr_nbtor_other0.0860.22648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2425
X-RAY DIFFRACTIONr_metal_ion_refined0.30.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.241
X-RAY DIFFRACTIONr_mcbond_it0.9071.54073
X-RAY DIFFRACTIONr_mcbond_other0.1511.51306
X-RAY DIFFRACTIONr_mcangle_it1.04725058
X-RAY DIFFRACTIONr_scbond_it1.75632535
X-RAY DIFFRACTIONr_scangle_it2.6384.52068
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 260 -
Rwork0.23 5106 -
obs-5366 99.93 %

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