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- PDB-4usq: Structure of flavin-containing monooxygenase from Cellvibrio sp. BR -

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Basic information

Entry
Database: PDB / ID: 4usq
TitleStructure of flavin-containing monooxygenase from Cellvibrio sp. BR
ComponentsPYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / FLAVIN / FAD / NAD(P)H
Function / homologyPyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / nucleotide binding / Alpha Beta / FLAVIN-ADENINE DINUCLEOTIDE / Pyridine nucleotide-disulfide oxidoreductase
Function and homology information
Biological speciesCELLVIBRIO SP. BR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsJensen, C.N. / Ali, S.T. / Allen, M.J. / Grogan, G.
CitationJournal: J.Mol.Catal. / Year: 2014
Title: Exploring Nicotinamide Cofactor Promiscuity in Nad(P)H-Dependent Flavin Containing Monooxygenases (Fmos) Using Natural Variation within the Phosphate Binding Loop. Structure and Activity of ...Title: Exploring Nicotinamide Cofactor Promiscuity in Nad(P)H-Dependent Flavin Containing Monooxygenases (Fmos) Using Natural Variation within the Phosphate Binding Loop. Structure and Activity of Fmos from Cellvibrio Sp. Br and Pseudomonas Stutzeri NF13
Authors: Jensen, C.N. / Ali, S.T. / Allen, M.J. / Grogan, G.
History
DepositionJul 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE
F: PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5394
Polymers78,9682
Non-polymers1,5712
Water73941
1
A: PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE
F: PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE
hetero molecules

A: PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE
F: PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,0798
Polymers157,9374
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13340 Å2
ΔGint-71.2 kcal/mol
Surface area50180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.410, 95.090, 92.370
Angle α, β, γ (deg.)90.00, 126.26, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2891, 0.006681, 0.9573), (0.003545, -1, 0.005909), (0.9573, 0.001685, -0.2891)
Vector: -6.997, 13.12, 9.55)

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Components

#1: Protein PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE / FLAVIN-CONTAINING MONOOXYGENASE


Mass: 39484.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO SP. BR (bacteria)
Description: TARGET INDENTIFIED USING BLAST SEARCH (SYNTHETIC GENE)
Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: I3IEE4, flavin-containing monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.74 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 7
Details: 1.5 M AMMONIUM SULFATE AND 1% (W/V)PROPAN-2-OL PH 7.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Mar 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.39→22.44 Å / Num. obs: 31344 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9
Reflection shellResolution: 2.39→2.45 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.9 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A9W

4a9w


Resolution: 2.39→22.35 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.876 / SU B: 11.485 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 0.458 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28662 1578 5 %RANDOM
Rwork0.24573 ---
obs0.24783 29763 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.213 Å2
Baniso -1Baniso -2Baniso -3
1-4.97 Å2-0 Å21.31 Å2
2---2.86 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.39→22.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5048 0 106 41 5195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195308
X-RAY DIFFRACTIONr_bond_other_d0.0030.024781
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9587298
X-RAY DIFFRACTIONr_angle_other_deg0.943310897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.125671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86222.664214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02315690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5141539
X-RAY DIFFRACTIONr_chiral_restr0.0860.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216090
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021273
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_it2.6713.7912696
X-RAY DIFFRACTIONr_mcbond_other2.673.7892695
X-RAY DIFFRACTIONr_mcangle_it3.9785.6793363
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7463.8872612
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.451 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 116 -
Rwork0.302 2185 -
obs--98.38 %

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