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- PDB-4hb9: Crystal structure of a putative FAD containing monooxygenase from... -

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Basic information

Entry
Database: PDB / ID: 4hb9
TitleCrystal structure of a putative FAD containing monooxygenase from Photorhabdus luminescens subsp. laumondii TTO1 (Target PSI-012791)
ComponentsSimilarities with probable monooxygenase
KeywordsOXIDOREDUCTASE / flavin / Structural genomics / New York Structural Genomics Research Consortium / NYSGRC / PSI / Aromatic ring hydroxylase-like / PSI-Biology
Function / homology
Function and homology information


NAD(P)-binding Rossmann-like domain / 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 / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 8/17
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsSampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: J.Biol.Chem. / Year: 2017
Title: Stilbene epoxidation and detoxification in a Photorhabdus luminescens -nematode symbiosis.
Authors: Park, H.B. / Sampathkumar, P. / Perez, C.E. / Lee, J.H. / Tran, J. / Bonanno, J.B. / Hallem, E.A. / Almo, S.C. / Crawford, J.M.
History
DepositionSep 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jun 15, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Similarities with probable monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,66412
Polymers46,2581
Non-polymers1,40611
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.008, 71.008, 157.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a probable monomer

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Components

#1: Protein Similarities with probable monooxygenase


Mass: 46258.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Strain: laumondii TTO1 / Gene: plu2236 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: Q7N4T1
#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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (MCSG3 #31; C7: 0.1 M Bis-Tris Propane:HCl pH 7.0, 1.0 M Ammonium Citrate Tribasic pH 7.0 ); Cryoprotection (30% Ethylene ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (MCSG3 #31; C7: 0.1 M Bis-Tris Propane:HCl pH 7.0, 1.0 M Ammonium Citrate Tribasic pH 7.0 ); Cryoprotection (30% Ethylene glycol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2012 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 35439 / Num. obs: 35439 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.2 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.102 / Net I/σ(I): 30.5
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 18.3 % / Mean I/σ(I) obs: 5.38 / Num. unique all: 1728 / Rsym value: 0.772 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0025refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
SCALEPACKdata scaling
SHELXCphasing
SHELXDphasing
SHELXE(HKL2MAP)model building
RefinementMethod to determine structure: SAD / Resolution: 1.93→48.56 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.795 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 1765 5 %RANDOM
Rwork0.1752 ---
obs0.1773 35385 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 102.69 Å2 / Biso mean: 28.9816 Å2 / Biso min: 14.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20.77 Å20 Å2
2--1.53 Å20 Å2
3----2.3 Å2
Refinement stepCycle: LAST / Resolution: 1.93→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 93 240 3259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193128
X-RAY DIFFRACTIONr_bond_other_d0.0020.022996
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9874246
X-RAY DIFFRACTIONr_angle_other_deg0.77836885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30723.971136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62515486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8681520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213503
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02720
LS refinement shellResolution: 1.932→1.982 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 137 -
Rwork0.196 2446 -
all-2583 -
obs--99.92 %

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