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- PDB-3c96: Crystal structure of the flavin-containing monooxygenase phzS fro... -

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Basic information

Entry
Database: PDB / ID: 3c96
TitleCrystal structure of the flavin-containing monooxygenase phzS from Pseudomonas aeruginosa. Northeast Structural Genomics Consortium target PaR240
ComponentsFlavin-containing monooxygenase
KeywordsOXIDOREDUCTASE / FAD / MONOOXYGENASE / PF01266 / NESG / PaR240 / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


5-methylphenazine-1-carboxylate 1-monooxygenase / 5-methylphenazine-1-carboxylate 1-monooxygenase (NADH) activity / monooxygenase activity / FAD binding
Similarity search - Function
D-Amino Acid Oxidase; Chain A, domain 2 - #30 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 5-methylphenazine-1-carboxylate 1-monooxygenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsVorobiev, S.M. / Chen, Y. / Seetharaman, J. / Wang, D. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the flavin-containing monooxygenase phzS from Pseudomonas aeruginosa.
Authors: Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Wang, D. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionFeb 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Flavin-containing monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5552
Polymers44,7701
Non-polymers7861
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.147, 65.261, 88.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS A MONOMER ACCORDING TO AGGREGATION SCREENING.

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Components

#1: Protein Flavin-containing monooxygenase


Mass: 44769.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PAO1 / 1C / PRS 101 / LMG 12228 / Gene: phzS, PA4217 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9HWG9
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.07 Å3/Da / Density % sol: 40.6 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 4.6
Details: 26% PEG 4000, 0.17M Ammonium acetate, 0.085M Sodium acetate, 15% Glycerol, 3% Glucose pH 4.6, MICROBATCH UNDER OIL, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97905, 0.97935, 0.96785
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979051
20.979351
30.967851
ReflectionResolution: 1.9→50 Å / Num. all: 55567 / Num. obs: 55567 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 42.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 14.4 / Num. unique all: 5786 / % possible all: 81.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→40.65 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 836931.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2627 4.9 %RANDOM
Rwork0.183 ---
obs0.183 53621 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.9231 Å2 / ksol: 0.405909 e/Å3
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2--2.49 Å20 Å2
3----1.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0 Å
Refinement stepCycle: LAST / Resolution: 1.9→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 53 278 3219
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.198 390 5 %
Rwork0.172 7487 -
obs--83.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4fad.parfad.top

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