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- PDB-4f07: Structure of the Styrene Monooxygenase Flavin Reductase (SMOB) fr... -

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Basic information

Entry
Database: PDB / ID: 4f07
TitleStructure of the Styrene Monooxygenase Flavin Reductase (SMOB) from Pseudomonas putida S12
ComponentsStyrene monooxygenase component 2
KeywordsOXIDOREDUCTASE / NADH-dependentFlavin Reductase / SMOA
Function / homology
Function and homology information


monooxygenase activity / FMN binding
Similarity search - Function
Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NITRATE ION / Styrene monooxygenase component 2
Similarity search - Component
Biological speciesPseudomonas (RNA similarity group I)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSazinsky, M.H. / Morrison, E. / Kantz, A. / Gassner, G.
CitationJournal: Biochemistry / Year: 2013
Title: Structure and Mechanism of Styrene Monooxygenase Reductase: New Insight into the FAD-Transfer Reaction.
Authors: Morrison, E. / Kantz, A. / Gassner, G.T. / Sazinsky, M.H.
History
DepositionMay 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Styrene monooxygenase component 2
B: Styrene monooxygenase component 2
C: Styrene monooxygenase component 2
D: Styrene monooxygenase component 2
E: Styrene monooxygenase component 2
F: Styrene monooxygenase component 2
G: Styrene monooxygenase component 2
H: Styrene monooxygenase component 2
I: Styrene monooxygenase component 2
J: Styrene monooxygenase component 2
K: Styrene monooxygenase component 2
L: Styrene monooxygenase component 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,06239
Polymers246,60312
Non-polymers10,45927
Water10,395577
1
A: Styrene monooxygenase component 2
D: Styrene monooxygenase component 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0509
Polymers41,1012
Non-polymers1,9497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-72 kcal/mol
Surface area14430 Å2
MethodPISA
2
B: Styrene monooxygenase component 2
C: Styrene monooxygenase component 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7966
Polymers41,1012
Non-polymers1,6954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-68 kcal/mol
Surface area14480 Å2
MethodPISA
3
E: Styrene monooxygenase component 2
F: Styrene monooxygenase component 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7345
Polymers41,1012
Non-polymers1,6333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-76 kcal/mol
Surface area14590 Å2
MethodPISA
4
G: Styrene monooxygenase component 2
H: Styrene monooxygenase component 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7966
Polymers41,1012
Non-polymers1,6954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-65 kcal/mol
Surface area14510 Å2
MethodPISA
5
I: Styrene monooxygenase component 2
J: Styrene monooxygenase component 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9548
Polymers41,1012
Non-polymers1,8536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-66 kcal/mol
Surface area14690 Å2
MethodPISA
6
K: Styrene monooxygenase component 2
L: Styrene monooxygenase component 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7345
Polymers41,1012
Non-polymers1,6333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-76 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.031, 130.031, 95.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Styrene monooxygenase component 2 /


Mass: 20550.254 Da / Num. of mol.: 12 / Mutation: A151T, S164G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Strain: Y2 / Gene: styB / Production host: Escherichia coli (E. coli) / References: UniProt: O33495
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 1.82 Å3/Da / Density % sol: 32.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris, 8.5, 1.7-1.9 M (NH4)2SO4, 200-300 mM NH4NO3, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2010
RadiationMonochromator: APS double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.884
11-h,-k,l20.116
ReflectionResolution: 2.23→50 Å / Num. all: 88220 / Num. obs: 87338 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rsym value: 0.0105 / Net I/σ(I): 13.4
Reflection shellResolution: 2.23→2.27 Å / Redundancy: 4.3 % / Rsym value: 0.068 / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1rz0

1rz0


Resolution: 2.3→48.47 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.893 / SU B: 7.331 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3913 4.9 %RANDOM
Rwork0.185 ---
obs0.188 76075 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13834 0 698 577 15109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02215040
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9622.00920573
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.88351835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49123.428566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94152152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.441572
X-RAY DIFFRACTIONr_chiral_restr0.130.22325
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111240
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2291.59269
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.123214871
X-RAY DIFFRACTIONr_scbond_it3.28735771
X-RAY DIFFRACTIONr_scangle_it4.8024.55700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 315 -
Rwork0.158 5456 -
obs--97.52 %

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