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- PDB-1usf: PUTATIVE STYRENE MONOOXYGENASE SMALL COMPONENT WITH BOUND NADP+ -

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Basic information

Entry
Database: PDB / ID: 1usf
TitlePUTATIVE STYRENE MONOOXYGENASE SMALL COMPONENT WITH BOUND NADP+
ComponentsPUTATIVE STYRENE MONOOXYGENASE SMALL COMPONENT
KeywordsOXYGENASE / FMN-BINDING PROTEIN / STRUCTURAL GENOMICS / MONOOXYGENASE / NADP / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / 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 MONONUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Monooxygenase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTahirov, T.H. / Inagaki, E. / Takahashi, H.
CitationJournal: To be Published
Title: Crystal Structure of Putative Styrene Monooxygenase Small Component from Thermus Thermophilus
Authors: Takahashi, H. / Inagaki, E. / Tahirov, T.H.
History
DepositionNov 21, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE STYRENE MONOOXYGENASE SMALL COMPONENT
B: PUTATIVE STYRENE MONOOXYGENASE SMALL COMPONENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,55310
Polymers39,4832
Non-polymers4,0708
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.684, 77.718, 63.748
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2080-

HOH

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Components

#1: Protein PUTATIVE STYRENE MONOOXYGENASE SMALL COMPONENT


Mass: 19741.439 Da / Num. of mol.: 2 / Fragment: FMN BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN WAS ISOLATED WITH BOUND FMN / Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P83818*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.7
Details: VAPOR DIFFUSION METHOD, 3.1 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH RESERVOIR SOLUTION (21% PEG4000, 0.1M SODIUM ACETATE PH 4.7) AND EQUILIBRATED AGAINST RESERVOIR SOLUTION AT ROOM ...Details: VAPOR DIFFUSION METHOD, 3.1 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH RESERVOIR SOLUTION (21% PEG4000, 0.1M SODIUM ACETATE PH 4.7) AND EQUILIBRATED AGAINST RESERVOIR SOLUTION AT ROOM TEMPERATURE (291 K). CRYSTAL WAS SOAKED FOR 4 HOURS IN RESERVOIR SOLUTION CONTAINING 0.005M NADP+, 21% PEG4000, AND 0.1M SODIUM ACETATE PH 4.7. CRYOPROTECTANT: 18% GLYCEROL, 24% PEG4000, 0.1M SODIUM ACETATE PH 4.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Feb 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 82839 / % possible obs: 95.2 % / Observed criterion σ(I): -0.5 / Redundancy: 3.91 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 29.9
Reflection shellResolution: 1.3→1.35 Å / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 3.09 / % possible all: 82.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1USC

1usc


Resolution: 1.3→29.49 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 938790.57 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 4158 5.1 %RANDOM
Rwork0.211 ---
obs0.211 82270 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.8191 Å2 / ksol: 0.35177 e/Å3
Displacement parametersBiso mean: 16 Å2
Baniso -1Baniso -2Baniso -3
1-4.9 Å20 Å20 Å2
2---4.61 Å20 Å2
3----0.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.3→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 182 344 3330
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.971.5
X-RAY DIFFRACTIONc_mcangle_it1.472
X-RAY DIFFRACTIONc_scbond_it1.662
X-RAY DIFFRACTIONc_scangle_it2.442.5
LS refinement shellResolution: 1.3→1.38 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.389 620 5.1 %
Rwork0.371 11565 -
obs--85.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3FMN.PARFMN.TOP
X-RAY DIFFRACTION4NAP.PARNAP.TOP

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