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- PDB-2i7g: Crystal Structure of Monooxygenase from Agrobacterium tumefaciens -

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Basic information

Entry
Database: PDB / ID: 2i7g
TitleCrystal Structure of Monooxygenase from Agrobacterium tumefaciens
ComponentsMonooxygenase
KeywordsOXIDOREDUCTASE / alpha-beta / TIM barrel / helix-bundle / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity
Similarity search - Function
Conserved hypothetical protein CHP03858, luciferase-like monooxygenase, putative / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Monooxygenase / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.73 Å
AuthorsKim, Y. / Xu, X. / Zheng, H. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2006
Title: The Crystal Structure of Monooxygenase from Agrobacterium tumefaciens
Authors: Kim, Y. / Xu, X. / Zheng, H. / Joachimiak, A. / Edwards, A. / Savchenko, A.
History
DepositionAug 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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: Monooxygenase
B: Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7386
Polymers83,3442
Non-polymers3944
Water11,890660
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-74 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.515, 139.974, 54.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Monooxygenase / / AGR_C_4197p


Mass: 41671.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UD21, UniProt: A9CI16*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-tris pH 5.5, 0.2M Ammonium sulfate, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97908 Å
DetectorType: SBC-3 / Detector: CCD / Date: Aug 22, 2006 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.73→29.37 Å / Num. all: 78621 / Num. obs: 78621 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.3
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2 / Num. unique all: 6883 / % possible all: 87.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
CCP4phasing
ARP/wARPmodel building
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.73→29.37 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.703 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.112
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.20199 7881 10.1 %RANDOM
Rwork0.1696 ---
all0.17292 70417 --
obs0.17292 70417 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.563 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2---0.6 Å20 Å2
3---1.96 Å2
Refinement stepCycle: LAST / Resolution: 1.73→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5344 0 22 660 6026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226174
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9738452
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7265822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14323.023301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.148151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7211567
X-RAY DIFFRACTIONr_chiral_restr0.1070.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024990
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.23435
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24343
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2686
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9281.53936
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41226231
X-RAY DIFFRACTIONr_scbond_it2.4132489
X-RAY DIFFRACTIONr_scangle_it3.6594.52221
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 523 -
Rwork0.3 4464 -
obs-4464 86.19 %
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)
11.9137-0.30520.14291.72210.32580.3994-0.0075-0.1480.02840.15070.0503-0.4062-0.01310.0294-0.0428-0.07440.0019-0.042-0.0727-0.0088-0.02978.34418.51946.918
21.89340.2322-0.1550.7595-0.15520.3379-0.01660.1030.1207-0.00660.03220.0890.019-0.0143-0.0156-0.063-0.00080.0032-0.0717-0.0046-0.102144.52922.76936.032
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 34321 - 364
2X-RAY DIFFRACTION2BB0 - 34421 - 365

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