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- PDB-2gjl: Crystal Structure of 2-nitropropane dioxygenase -

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Basic information

Entry
Database: PDB / ID: 2gjl
TitleCrystal Structure of 2-nitropropane dioxygenase
Componentshypothetical protein PA1024Hypothesis
KeywordsOXIDOREDUCTASE / 2-nitropropane dioxygenase / 2-nitropropane / FMN
Function / homology
Function and homology information


NADH:quinone reductase (non-electrogenic) / nitronate monooxygenase activity / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity / nucleotide binding
Similarity search - Function
Nitronate monooxygenase / Nitronate monooxygenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NADH:quinone reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsSuh, S.W.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of 2-Nitropropane Dioxygenase Complexed with FMN and Substrate: identification of the catalytic base
Authors: Ha, J.Y. / Min, J.Y. / Lee, S.K. / Kim, H.S. / Kim, J. / Kim, K.H. / Lee, H.H. / Kim, H.K. / Yoon, H.J. / Suh, S.W.
History
DepositionMar 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: hypothetical protein PA1024
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3172
Polymers34,8611
Non-polymers4561
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein PA1024
hetero molecules

A: hypothetical protein PA1024
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6344
Polymers69,7222
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area5910 Å2
ΔGint-40 kcal/mol
Surface area24160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.546, 93.546, 80.704
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a monomer

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Components

#1: Protein hypothetical protein PA1024 / Hypothesis / 2-nitropropane dioxygeanse


Mass: 34860.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PA01 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9I4V0, EC: 1.13.11.32
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES at pH 7.0, 5%(w/v) tacsimate at pH 7.0, 10%(w/v) PEG MME 5000, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A10.97915, 0.97948, 0.95000
SYNCHROTRONPAL/PLS 6B21
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDDec 2, 2003mirrors
BRUKER PROTEUM 3002CCDMar 14, 2004mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Numerical link type Si(111) double crystal monochromator, liquid nitrogen coolingMADMx-ray1
2Double Crystal MonochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.979481
30.951
411
Reflection

D res low: 50 Å

IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
19.61437160.0770.872.3617169100
29.31428710.0710.662.3617199100
37.21138300.0840.862.51445199.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obsChi squared
5.0850182099.710.0411.936
4.035.08174510010.0441.761
3.534.03171710010.0531.326
3.23.53171510010.0670.911
2.973.2170810010.0960.667
2.82.97170010010.1290.51
2.662.8168310010.1720.446
2.542.66169410010.2160.407
2.442.54169210010.2710.39
2.362.44169510010.3590.359
5.0850182499.720.0361.509
4.035.08174510020.0371.181
3.534.03171610020.0450.894
3.23.53172110020.0610.663
2.973.2171010020.090.52
2.82.97169310020.1280.425
2.662.8169310020.1730.385
2.542.66169510020.220.352
2.442.54170810020.2890.391
2.362.44169410020.3830.345
5.3850154399.730.0454.495
4.275.38146510030.0450.841
3.734.27145610030.050.695
3.393.73145210030.0670.538
3.153.39145310030.0970.433
2.963.15143210030.1420.373
2.822.96142110030.2030.334
2.692.82143110030.2740.319
2.592.69140899.230.3340.319
2.52.59139097.230.3920.33
ReflectionResolution: 2→15 Å / Num. obs: 27790 / % possible obs: 99.5 % / Rmerge(I) obs: 0.074 / Χ2: 1.041 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID
2-2.071000.27927530.6141,2
2.07-2.151000.22627470.641,2
2.15-2.251000.1627690.6621,2
2.25-2.371000.13727590.7081,2
2.37-2.521000.10427840.7441,2
2.52-2.711000.08927610.8961,2
2.71-2.981000.0727841.0561,2
2.98-3.411000.05327981.291,2
3.41-4.2899.40.03928261.7471,2
4.28-1596.20.04228092.891,2

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.5 Å / D res low: 20 Å / FOM : 0.68 / Reflection: 14435
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97915.68-5.95
13 wavelength20.97493.17-9.94
13 wavelength30.953.88-2.49
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
154.74744.8715.502SE33.81.04
27.53162.6361.874SE31.50.95
3-18.45344.18313.553SE30.80.96
410.64775.3984.039SE351.04
54.96966.1241.478SE45.40.96
670.41925.1520.766SE44.61.04
7-34.18660.0424.913SE44.30.97
Phasing MAD shell
Resolution (Å)FOM Reflection
8.52-200.93777
5.54-8.520.911225
4.38-5.540.91532
3.74-4.380.851779
3.31-3.740.782014
3-3.310.632184
2.77-30.52372
2.58-2.770.362552
Phasing dmFOM : 0.73 / FOM acentric: 0.74 / FOM centric: 0.67 / Reflection: 14409 / Reflection acentric: 12813 / Reflection centric: 1596
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-19.6540.970.980.94643473170
4.5-7.10.940.960.8719531646307
3.6-4.50.920.930.8324232143280
3.1-3.60.840.850.7324242184240
2.7-3.10.630.650.4742993914385
2.5-2.70.420.430.2926672453214

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVE2.03phasing
CNSrefinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
RefinementMethod to determine structure: MAD / Resolution: 2→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.227 2658 9.7 %
Rwork0.191 --
obs-26759 97.4 %
Solvent computationBsol: 108.07 Å2
Displacement parametersBiso mean: 24.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.859 Å2-1.174 Å20 Å2
2---1.859 Å20 Å2
3---3.718 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 31 288 2738
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2831.5
X-RAY DIFFRACTIONc_scbond_it2.2282
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scangle_it3.2642.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3fmn_mod.par

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