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- PDB-6hns: Structure of Nitrincola lacisaponensis flavin-containing monooxyg... -

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Basic information

Entry
Database: PDB / ID: 6hns
TitleStructure of Nitrincola lacisaponensis flavin-containing monooxygenase (FMO) in complex with FAD and NADP+
ComponentsSmall molecule metabolism
KeywordsFLAVOPROTEIN / drug metabolism / monooxygenase / thermostability / indigo
Function / homology
Function and homology information


trimethylamine monooxygenase / N,N-dimethylaniline monooxygenase activity / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
: / Flavin monooxygenase FMO / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Trimethylamine monooxygenase
Similarity search - Component
Biological speciesNitrincola lacisaponensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsFiorentini, F. / Mattevi, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italy
CitationJournal: Appl. Microbiol. Biotechnol. / Year: 2019
Title: Characterization of a thermostable flavin-containing monooxygenase from Nitrincola lacisaponensis (NiFMO).
Authors: Loncar, N. / Fiorentini, F. / Bailleul, G. / Savino, S. / Romero, E. / Mattevi, A. / Fraaije, M.W.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 6, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small molecule metabolism
B: Small molecule metabolism
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3428
Polymers105,2352
Non-polymers3,1076
Water8,377465
1
A: Small molecule metabolism
hetero molecules

A: Small molecule metabolism
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3428
Polymers105,2352
Non-polymers3,1076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area9290 Å2
ΔGint-47 kcal/mol
Surface area30590 Å2
MethodPISA
2
B: Small molecule metabolism
hetero molecules

B: Small molecule metabolism
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3428
Polymers105,2352
Non-polymers3,1076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area9170 Å2
ΔGint-49 kcal/mol
Surface area30180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.057, 125.611, 144.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-650-

HOH

21A-826-

HOH

31B-806-

HOH

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Components

#1: Protein Small molecule metabolism


Mass: 52617.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrincola lacisaponensis (bacteria) / Gene: ADINL_0099 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A063Y6V3
#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: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 8 / Details: 0.2 Mg formate, 20% W/V PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.84→47.48 Å / Num. obs: 93414 / % possible obs: 99.2 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.7
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.849 / Num. unique obs: 4431 / CC1/2: 0.585 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VQ7

2vq7


Resolution: 1.84→47.48 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.332 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21724 4601 4.9 %RANDOM
Rwork0.18149 ---
obs0.18325 88765 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.84→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7227 0 204 465 7896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0147677
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176325
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.69510468
X-RAY DIFFRACTIONr_angle_other_deg1.0241.65614814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1935883
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34421.849449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.638151149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4771551
X-RAY DIFFRACTIONr_chiral_restr0.090.2934
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021642
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_it1.8152.5223538
X-RAY DIFFRACTIONr_mcbond_other1.8142.5223537
X-RAY DIFFRACTIONr_mcangle_it2.3563.7734419
X-RAY DIFFRACTIONr_mcangle_other2.3553.7744420
X-RAY DIFFRACTIONr_scbond_it2.5392.744135
X-RAY DIFFRACTIONr_scbond_other2.5382.7394136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7044.0216049
X-RAY DIFFRACTIONr_long_range_B_refined4.49528.9099204
X-RAY DIFFRACTIONr_long_range_B_other4.48228.7959129
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 337 -
Rwork0.29 6332 -
obs--97.32 %

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