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- PDB-2h0u: Crystal structure of NAD(P)H-flavin oxidoreductase from Helicobac... -

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Basic information

Entry
Database: PDB / ID: 2h0u
TitleCrystal structure of NAD(P)H-flavin oxidoreductase from Helicobacter pylori
ComponentsNADPH-flavin oxidoreductase
KeywordsOXIDOREDUCTASE / NAD(P)H-flavin oxidoreductase / Helicobacter pylori / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / identical protein binding
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NAD(P)H nitroreductase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsChang, C. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of NAD(P)H-flavin oxidoreductase from Helicobacter pylori
Authors: Chang, C. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMay 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3462
Polymers25,8901
Non-polymers4561
Water3,891216
1
A: NADPH-flavin oxidoreductase
hetero molecules

A: NADPH-flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6924
Polymers51,7802
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9330 Å2
ΔGint-61 kcal/mol
Surface area16970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.035, 87.178, 94.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-314-

HOH

21A-318-

HOH

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Components

#1: Protein NADPH-flavin oxidoreductase / NADP / H-flavin oxidoreductase


Mass: 25889.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: frxA / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivatives / References: UniProt: Q7BGI8
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na(OAC), 27% PEG2KMME, 5mM FMN, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. all: 18453 / Num. obs: 18268 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rsym value: 0.087 / Net I/σ(I): 45
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 12.8 / Num. unique all: 1685 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→47.51 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.984 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22054 919 5.1 %RANDOM
Rwork0.17771 ---
all0.17988 17063 --
obs0.17988 17063 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.295 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.52 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 31 216 1842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221660
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.972240
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7075194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20324.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66515303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8191510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021236
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2781
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21158
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4681.51012
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.54121566
X-RAY DIFFRACTIONr_scbond_it3.0263799
X-RAY DIFFRACTIONr_scangle_it4.3384.5674
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 66 -
Rwork0.159 1233 -
obs--99.92 %
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)
12.9091-0.1366-0.53061.07020.25351.4882-0.0421-0.1879-0.17860.15820.047-0.04170.16160.1513-0.0049-0.05740.0119-0.0191-0.0620.0207-0.0744.5736.7335.565
20.1854-0.0476-0.1610.1044-0.01970.5710.08740.0459-0.0655-0.02550.0015-0.101-0.0490.1606-0.08880.0354-0.00170.01840.0375-0.01070.05448.26215.94115.475
31.5594-0.364-0.02561.68562.14844.17750.09920.15820.1021-0.0846-0.01690.2364-0.3518-0.5945-0.08220.06050.0970.00960.01480.0889-0.0266-12.74827.0710.063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 182 - 18
2X-RAY DIFFRACTION1AA199 - 216199 - 216
3X-RAY DIFFRACTION2AA19 - 8719 - 87
4X-RAY DIFFRACTION2AA131 - 198131 - 198
5X-RAY DIFFRACTION3AA88 - 13088 - 130

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