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- PDB-2fre: The crystal structure of the oxidoreductase containing FMN -

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Basic information

Entry
Database: PDB / ID: 2fre
TitleThe crystal structure of the oxidoreductase containing FMN
ComponentsNAD(P)H-flavin oxidoreductase
KeywordsOXIDOREDUCTASE / FMN / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NAD(P)H-flavin oxidoreductase / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the oxidoreductase containing FMN from Agrobacterium tumefaciens
Authors: Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJan 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P)H-flavin oxidoreductase
B: NAD(P)H-flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1364
Polymers45,2232
Non-polymers9132
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-55 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.337, 77.337, 151.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThis protein existed as dimer. The deposited Mol.A and Mol.B represent the dimer in the asymmetric unit.

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Components

#1: Protein NAD(P)H-flavin oxidoreductase


Mass: 22611.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / ATCC 33970 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UJB5, UniProt: A9CKT4*PLUS
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.15M Potassium Bromide, 36% PEG2KMME, 10mM FMN, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→68.84 Å / Num. all: 35142 / Num. obs: 34404 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16.6 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 25.86
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2578 / % possible all: 94.43

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→68.84 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.562 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.151 / ESU R Free: 0.134
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 1803 5 %RANDOM
Rwork0.18259 ---
all0.18407 35142 --
obs0.18407 34404 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.032 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.9→68.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 62 405 3614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223309
X-RAY DIFFRACTIONr_bond_other_d0.0010.022889
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9594504
X-RAY DIFFRACTIONr_angle_other_deg0.79536735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67123.725153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49715517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.151518
X-RAY DIFFRACTIONr_chiral_restr0.0710.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
X-RAY DIFFRACTIONr_nbd_refined0.2130.2768
X-RAY DIFFRACTIONr_nbd_other0.1930.22998
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21603
X-RAY DIFFRACTIONr_nbtor_other0.0820.21782
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2302
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.222
X-RAY DIFFRACTIONr_mcbond_it0.9911.52394
X-RAY DIFFRACTIONr_mcbond_other0.171.5800
X-RAY DIFFRACTIONr_mcangle_it1.0923189
X-RAY DIFFRACTIONr_scbond_it1.9131584
X-RAY DIFFRACTIONr_scangle_it2.5814.51315
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 110 -
Rwork0.213 2435 -
obs-2435 94.43 %
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)
10.85520.1477-0.50841.0086-0.06411.4653-0.0388-0.0641-0.17890.0940.01650.11770.071-0.01520.0223-0.03970.0050.0153-0.0471-0.0011-0.088821.88211.05146.518
20.92610.1622-0.13831.23540.10311.3779-0.02520.2298-0.0277-0.21380.04990.064-0.15230.0547-0.0247-0.0118-0.0191-0.0032-0.0061-0.0255-0.155427.75120.1331.056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 501 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 151101 - 151
4X-RAY DIFFRACTION1AA152 - 199152 - 199
5X-RAY DIFFRACTION2BB1 - 501 - 50
6X-RAY DIFFRACTION2BB51 - 10051 - 100
7X-RAY DIFFRACTION2BB101 - 151101 - 151
8X-RAY DIFFRACTION2BB152 - 195152 - 195

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