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- PDB-4aeo: Structure of Xenobiotic Reductase B from Pseudomonas putida in co... -

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Basic information

Entry
Database: PDB / ID: 4aeo
TitleStructure of Xenobiotic Reductase B from Pseudomonas putida in complex with TNT
ComponentsXENOBIOTIC REDUCTASE B
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 2,4,6-TRINITROTOLUENE / Xenobiotic reductase B
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCarvalho, A.L. / Mukhopadhyay, A. / Romao, M.J. / Bursakov, S. / Kladova, A. / Ramos, J.L. / van Dillewijn, P.
CitationJournal: To be Published
Title: Structural Determinants of Aromatic Ring Reduction in the Xenobiotic Reductase B from Pseudomonas Putida
Authors: Carvalho, A.L. / Mukhopadhyay, A. / Bonifacio, C. / Romao, M.J. / Bursakov, S. / Kladova, A. / Ramos, J.L. / Van Dillewijn, P.
History
DepositionJan 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XENOBIOTIC REDUCTASE B
B: XENOBIOTIC REDUCTASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,49610
Polymers78,7482
Non-polymers1,7478
Water13,727762
1
A: XENOBIOTIC REDUCTASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3426
Polymers39,3741
Non-polymers9685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: XENOBIOTIC REDUCTASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1544
Polymers39,3741
Non-polymers7803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.180, 105.320, 106.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9999, 0.0095, 0.0097), (0.0101, -0.998, -0.0626), (0.0091, 0.0627, -0.998)
Vector: -33.4947, 1.3063, 3.9597)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein XENOBIOTIC REDUCTASE B / OLD YELLOW ENZYME


Mass: 39374.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) PSEUDOMONAS PUTIDA KT2440 (bacteria) / References: UniProt: Q88PD0

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Non-polymers , 5 types, 770 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TNL / 2,4,6-TRINITROTOLUENE / TNT / TNT


Mass: 227.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5N3O6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 762 / 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→25.6 Å / Num. obs: 79931 / % possible obs: 95.5 % / Observed criterion σ(I): 2.7 / Redundancy: 5.6 % / Biso Wilson estimate: 11.44 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.7 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→25.565 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 18.19 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.205 8018 10.04 %
Rwork0.1719 --
obs0.1752 79856 95.15 %
Solvent computationShrinkage radii: 0.17 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.555 Å2 / ksol: 0.472 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5197 Å20 Å20 Å2
2--3.5395 Å20 Å2
3----1.0199 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 115 762 6181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085585
X-RAY DIFFRACTIONf_angle_d1.167637
X-RAY DIFFRACTIONf_dihedral_angle_d14.4022042
X-RAY DIFFRACTIONf_chiral_restr0.07818
X-RAY DIFFRACTIONf_plane_restr0.0061020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.26772730.21672306X-RAY DIFFRACTION93
1.7193-1.73950.25022800.20282289X-RAY DIFFRACTION94
1.7395-1.76080.25042650.20082320X-RAY DIFFRACTION93
1.7608-1.7830.24872650.19482307X-RAY DIFFRACTION93
1.783-1.80650.25832750.19262295X-RAY DIFFRACTION92
1.8065-1.83120.23752310.18082312X-RAY DIFFRACTION93
1.8312-1.85740.23712590.17172298X-RAY DIFFRACTION92
1.8574-1.88510.21242520.1772307X-RAY DIFFRACTION93
1.8851-1.91450.21472330.16732339X-RAY DIFFRACTION92
1.9145-1.94590.22012850.16712286X-RAY DIFFRACTION93
1.9459-1.97950.21042670.16112294X-RAY DIFFRACTION92
1.9795-2.01540.19582560.15662316X-RAY DIFFRACTION94
2.0154-2.05420.21012610.15442344X-RAY DIFFRACTION93
2.0542-2.09610.18382300.15492340X-RAY DIFFRACTION93
2.0961-2.14170.19392530.15252351X-RAY DIFFRACTION94
2.1417-2.19150.19952750.1432358X-RAY DIFFRACTION94
2.1915-2.24620.19432640.14842337X-RAY DIFFRACTION94
2.2462-2.30690.18742840.15492334X-RAY DIFFRACTION94
2.3069-2.37480.18922550.1542395X-RAY DIFFRACTION95
2.3748-2.45140.20042440.15112432X-RAY DIFFRACTION95
2.4514-2.53890.18632740.16272388X-RAY DIFFRACTION96
2.5389-2.64040.20122550.16132437X-RAY DIFFRACTION96
2.6404-2.76050.19262450.16562482X-RAY DIFFRACTION97
2.7605-2.90580.19672960.15952482X-RAY DIFFRACTION98
2.9058-3.08760.18312890.16792505X-RAY DIFFRACTION100
3.0876-3.32550.19172720.17532547X-RAY DIFFRACTION100
3.3255-3.65930.22012630.18492600X-RAY DIFFRACTION100
3.6593-4.18680.1722890.16512575X-RAY DIFFRACTION100
4.1868-5.26740.21493080.18512567X-RAY DIFFRACTION100
5.2674-25.56740.22753200.23142695X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.116-0.09570.080.1007-0.01930.09540.0073-0.015-0.0254-0.02460.00480.0290.0139-0.0049-00.05010.0066-0.00890.0514-0.00430.0628-22.2313-6.33212.0454
20.0575-0.02420.0010.02850.03340.0895-0.0174-0.0165-0.0594-0.08310.07450.10670.0539-0.04370.0010.0709-0.007-0.00950.05740.01660.1044-17.1738-24.63478.1737
30.04140.0207-0.02340.0097-0.00820.0205-0.00640.04380.0127-0.0142-0.007-0.0210.0548-0.0073-0.00150.0740.0172-0.00690.0689-0.00710.0793-8.0019-17.5596-4.9369
40.01620.0012-0.01460.0051-0.00590.01480.04560.0602-0.0754-0.0177-0.01970.02680.04020.009800.0741-0.0104-0.01360.0514-0.00060.0675-11.0531-13.40616.1757
50.0334-0.02840.00720.0211-0.00160.01140.02420.0476-0.03280.0158-0.0041-0.0380.0483-0.028700.09730.0163-0.01620.0697-0.00770.0853-0.0067-18.33445.4269
60.0390.0004-0.00020.0146-0.00390.0110.0270.00260.01540.0084-0.0111-0.0051-0.0315-0.001100.09160.0018-0.01690.07480.00390.0778-7.6326-12.110713.3358
70.0485-0.0030.05120.0387-0.01570.0544-0.0222-0.0669-0.01330.060.0108-0.01130.0012-0.006300.05860.00610.00020.08080.00030.0483-4.8681-5.266216.4525
80.2425-0.24490.07840.2645-0.04620.1315-0.0236-0.1984-0.05120.080.04520.1001-0.0232-0.08240.05680.05560.02150.00650.1098-0.00620.0301-26.6991-0.186516.0759
90.08160.0398-0.04710.0709-0.07340.07230.0087-0.019-0.0072-0.02340.02430.0685-0.0119-0.01940.0020.05290.00590.00380.05910.00650.053412.00182.8915-8.9919
100.04770.0010.00510.01220.00560.01970.0118-0.05580.0350.0359-0.0280.0379-0.0142-0.035300.06220.010.01040.0765-0.00080.061310.29339.92850.7807
110.0795-0.00460.03630.01720.02140.1864-0.0019-0.01020.10850.02430.0160.0305-0.0384-0.07470.00580.0670.03240.02580.02090.010.112815.651117.8511-7.209
120.0435-0.0377-0.06830.03940.04210.1340.05230.00570.04570.11330.06360.1392-0.1137-0.09260.04180.1140.00570.00020.0980.02650.141517.977529.3335-14.0946
130.13740.04450.01830.0271-0.0290.09430.0017-0.165-0.04290.0960.0166-0.1417-0.13730.02560.02010.0619-0.003-0.00460.0813-0.01670.06725.879416.09391.863
140.008-0.00310.00820.0043-0.00940.0062-0.0169-0.0068-0.0035-0.0044-0.0162-0.0448-0.0106-0.0234-0.02030.04310.0040.00540.03930.01180.044622.555112.4558-9.6185
150.0238-0.01180.01760.020.01750.0547-0.0153-0.01960.0070.0208-0.026-0.1116-0.0490.0381-0.00010.075-0.0020.00930.07010.01660.080633.679217.1135-8.6978
160.0601-0.0274-0.0220.0245-0.00630.0089-0.0153-0.0087-0.0113-0.01170.0005-0.00790.0095-0.0106-0.03940.060.00910.0090.06240.01830.04625.774711.5261-16.9358
170.06190.0152-0.04120.05580.02480.0358-0.06340.04960.0391-0.0061-0.0101-0.0249-0.0432-0.0289-0.00080.0671-0.00150.00470.08320.00510.057230.17156.6533-19.6414
180.0149-0.0015-0.0130.00750.00360.0098-0.02420.0713-0.0318-0.0846-0.00230.01080.0152-0.021-00.06910.0075-0.00690.07950.0040.063325.58651.4692-21.8609
190.0088-0.01250.00510.02820.01720.01610.01590.05670.0418-0.05720.01890.01630.0268-0.0275-00.0762-0.005-0.0070.10.00150.058413.1908-3.781-21.9904
200.01710.0071-0.01260.0249-0.00590.011-0.06370.03910.005-0.02110.06110.1286-0.0154-0.0657-0.04330.08060.00530.00090.10680.01370.0783-0.38554.1808-17.9907
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:90)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 91:144)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 145:164)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 165:184)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 185:217)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 218:239)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 240:289)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 290:350)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 2:63)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 64:90)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 91:115)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 116:144)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 145:164)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 165:184)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 185:217)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 218:239)
17X-RAY DIFFRACTION17CHAIN B AND (RESSEQ 240:270)
18X-RAY DIFFRACTION18CHAIN B AND (RESSEQ 271:289)
19X-RAY DIFFRACTION19CHAIN B AND (RESSEQ 290:322)
20X-RAY DIFFRACTION20CHAIN B AND (RESSEQ 323:350)

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