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- PDB-3d1l: Crystal structure of putative NADP oxidoreductase BF3122 from Bac... -

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Basic information

Entry
Database: PDB / ID: 3d1l
TitleCrystal structure of putative NADP oxidoreductase BF3122 from Bacteroides fragilis
ComponentsPutative NADP oxidoreductase BF3122
KeywordsOXIDOREDUCTASE / putative NADP oxidoreductase / BF3122 / Bacteroides fragilis / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


ProC-like, C-terminal domain / Domain of unknown function DUF2520 / TM1727-like, C-terminal domain superfamily / Domain of unknown function (DUF2520) / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...ProC-like, C-terminal domain / Domain of unknown function DUF2520 / TM1727-like, C-terminal domain superfamily / Domain of unknown function (DUF2520) / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-MERCAPTO-PROPION ALDEHYDE / Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsChang, C. / Hendricks, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative NADP oxidoreductase BF3122 from Bacteroides fragilis.
Authors: Chang, C. / Hendricks, R. / Abdullah, J. / Joachimiak, A.
History
DepositionMay 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative NADP oxidoreductase BF3122
B: Putative NADP oxidoreductase BF3122
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2215
Polymers61,0052
Non-polymers2163
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-62.4 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.995, 154.995, 54.313
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Putative NADP oxidoreductase BF3122


Mass: 30502.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF3122 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q5LAQ6
#2: Chemical ChemComp-MPR / 2-MERCAPTO-PROPION ALDEHYDE


Mass: 90.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6OS
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8 M Ammonium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97949 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 7, 2008
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 36340 / Num. obs: 32819 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 58.98
Reflection shellResolution: 2.19→2.22 Å / Redundancy: 5 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.03 / Num. unique all: 714 / % possible all: 84.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.19→33.71 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.992 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23905 1662 5.1 %RANDOM
Rwork0.18532 ---
all0.18801 32697 --
obs0.18801 32697 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.122 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20 Å2
2---1.53 Å20 Å2
3---3.07 Å2
Refinement stepCycle: LAST / Resolution: 2.19→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4079 0 11 231 4321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224316
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9665871
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5395549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13123.886211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37115753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.011533
X-RAY DIFFRACTIONr_chiral_restr0.0990.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023304
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.22058
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22949
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6771.52734
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14224278
X-RAY DIFFRACTIONr_scbond_it1.78831785
X-RAY DIFFRACTIONr_scangle_it2.6594.51578
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 110 -
Rwork0.235 2030 -
obs-2140 86.82 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.0774-0.6585-1.210112.11471.62854.6321-0.2721-0.3908-0.17441.5590.5435-1.01850.5080.9072-0.27140.04410.1494-0.25320.0383-0.0258-0.2144-15.3314-7.914949.9731
21.765-1.53230.67586.3288-0.13174.6361-0.18510.0468-0.20820.44630.49230.58830.06180.0703-0.3073-0.0971-0.0190.0519-0.02840.0852-0.1071-28.0396-5.068442.1079
36.14631.99230.912511.9325-1.02623.4266-0.0244-0.08710.46641.06910.3839-1.1365-0.49060.3499-0.3594-0.0184-0.0767-0.051-0.0665-0.1698-0.0871-17.45518.675544.9322
428.091310.1519-20.15233.6688-7.282814.4569-0.60140.72150.1591-0.73060.592-0.12220.3952-0.60480.0094-0.0449-0.17990.0681-0.01790.0004-0.0309-20.013912.453130.9347
55.2641.8089-1.08092.36010.31011.2219-0.04940.1679-0.53240.17920.0589-0.21320.1785-0.0419-0.0095-0.0338-0.04190.0313-0.1087-0.0547-0.02114.227218.657624.2364
613.0063-0.91890.36074.82020.08432.7474-0.18881.2503-0.7861-0.34790.16840.38980.542-0.52550.0205-0.1171-0.24340.0142-0.002-0.1202-0.1243-11.118312.888417.1645
74.4739-1.46910.55063.6053-0.02493.4559-0.1407-0.29130.07660.3450.043-0.14430.0329-0.17030.0977-0.08850.01-0.0449-0.0634-0.1179-0.056212.69643.966238.1204
80.92820.7931-0.65045.04721.31342.3349-0.24160.21590.2802-0.57160.0718-0.3257-0.2375-0.25710.1698-0.0621-0.004-0.0272-0.1008-0.06470.058417.392747.583424.1572
92.84891.9636-0.63484.1750.27751.41820.0244-0.0833-0.17610.15850.1324-0.62280.2523-0.0883-0.1568-0.10930.0139-0.0245-0.1211-0.08960.054617.892631.079730.3923
1021.63025.6957-3.68138.2731-0.50070.8783-0.38930.72350.1078-0.69090.363-0.20210.2276-0.25380.02640.0153-0.02920.0681-0.0171-0.0427-0.095713.083128.704516.916
115.34942.16740.06083.16250.51030.73610.19210.0454-0.00160.308-0.21170.31550.3271-0.07190.01960.0264-0.0780.0661-0.1012-0.0251-0.0411-6.373619.018430.3252
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 56
2X-RAY DIFFRACTION2A57 - 117
3X-RAY DIFFRACTION3A118 - 163
4X-RAY DIFFRACTION4A164 - 175
5X-RAY DIFFRACTION5A176 - 216
6X-RAY DIFFRACTION6B217 - 262
7X-RAY DIFFRACTION7B4 - 56
8X-RAY DIFFRACTION8B57 - 117
9X-RAY DIFFRACTION9B118 - 163
10X-RAY DIFFRACTION10B164 - 175
11X-RAY DIFFRACTION11B176 - 216

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