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- PDB-4hm7: Naphthalene 1,2-Dioxygenase bound to styrene -

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Basic information

Entry
Database: PDB / ID: 4hm7
TitleNaphthalene 1,2-Dioxygenase bound to styrene
Components(Naphthalene 1,2-dioxygenase subunit ...) x 2
KeywordsOxidoreductase/Oxidoreductase inhibitor / Oxidoreductase-Oxidoreductase inhibitor complex
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 / ethenylbenzene / Naphthalene 1,2-dioxygenase system, large oxygenase component / Naphthalene 1,2-dioxygenase system, small oxygenase component
Similarity search - Component
Biological speciesPseudomonas sp. C18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFerraro, D.J. / Ramaswamy, S.
CitationJournal: To be Published
Title: Naphthalene 1,2-Dioxygenase bound to styrene
Authors: Ferraro, D.J. / Ramaswamy, S.
History
DepositionOct 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,85017
Polymers72,6332
Non-polymers1,21715
Water11,818656
1
A: Naphthalene 1,2-dioxygenase subunit alpha
B: Naphthalene 1,2-dioxygenase subunit beta
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)221,55051
Polymers217,9006
Non-polymers3,65045
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 area37790 Å2
ΔGint-268 kcal/mol
Surface area58810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.835, 139.835, 208.029
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-1333-

HOH

21A-1561-

HOH

31B-1163-

HOH

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Components

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

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


Mass: 49664.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. C18 (bacteria) / Strain: NCIB 9816-4 / Gene: doxB, NC_004999.1 / 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 subunit beta / / 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. C18 (bacteria) / Strain: NCIB 9816-4 / Gene: doxD, NC_004999.1 / 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, 671 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / 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-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Chemical ChemComp-SYN / ethenylbenzene / styrene / Styrene


Mass: 104.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 279.15 K / Method: vapor diffusion / pH: 5
Details: 1.9-2.2 M AMMONIUM SULFATE, 4-6%, DIOXANE, 0.1 M MES, pH 5.0, VAPOR DIFFUSION, temperature 279.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.04 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Nov 1, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.5→15.98 Å / Num. obs: 121577 / % possible obs: 97.8 % / Redundancy: 4.07 % / Rmerge(I) obs: 0.057 / Χ2: 0.99 / Net I/σ(I): 12.6 / Scaling rejects: 3737
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.5-1.552.880.4362.730116104021.2184.5
1.55-1.623.630.3743.342994117931.1395.6
1.62-1.694.150.3183.951770123991.11100
1.69-1.784.190.2514.751914123231.06100
1.78-1.894.210.1816.152452123711.03100
1.89-2.034.230.1218.552749123710.99100
2.03-2.244.260.08311.853294124190.92100
2.24-2.564.290.06115.753769124400.88100
2.56-3.224.330.04122.754421125010.8399.8
3.22-15.984.30.0263954785125580.8898.4

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Processing

Software
NameVersionClassificationNB
d*TREK9.2LDzdata reduction
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→15.981 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8859 / SU ML: 0.17 / σ(F): 1.09 / Phase error: 19.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1937 6127 5.05 %
Rwork0.157 --
obs0.1588 121500 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.56 Å2 / Biso mean: 20.1602 Å2 / Biso min: 4.79 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5073 0 65 656 5794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065266
X-RAY DIFFRACTIONf_angle_d1.1537106
X-RAY DIFFRACTIONf_chiral_restr0.076740
X-RAY DIFFRACTIONf_plane_restr0.004927
X-RAY DIFFRACTIONf_dihedral_angle_d13.771903
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5170.3232980.29925846614476
1.517-1.53490.31733480.29196086643480
1.5349-1.55360.31893500.27396254660482
1.5536-1.57320.3043640.26376649701387
1.5732-1.59390.29333940.24057195758994
1.5939-1.61570.25734120.22857591800399
1.6157-1.63880.26184220.210876758097100
1.6388-1.66320.23473660.195877538119100
1.6632-1.68920.2494320.18477028134100
1.6892-1.71680.20763970.176976418038100
1.7168-1.74640.22863890.167776478036100
1.7464-1.77810.21514370.173676648101100
1.7781-1.81230.23743980.16876808078100
1.8123-1.84920.21154000.156476448044100
1.8492-1.88940.20134320.145776938125100
1.8894-1.93320.18593450.140677788123100
1.9332-1.98150.19594160.1476058021100
1.9815-2.0350.19054240.139776388062100
2.035-2.09470.19633380.138277598097100
2.0947-2.16220.17494250.134976748099100
2.1622-2.23930.16034010.131776468047100
2.2393-2.32870.1864120.135676798091100
2.3287-2.43430.18793810.135477028083100
2.4343-2.56220.16294730.135675588031100
2.5622-2.72190.17863780.144577388116100
2.7219-2.93090.19354480.15276128060100
2.9309-3.22370.19984360.156476278063100
3.2237-3.68520.16874030.14797647805099
3.6852-4.62420.16143930.13887580797398
4.6242-15.9820.1713580.16717434779296

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