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- PDB-2xlr: Joint-functions of protein residues and NADP(H) in oxygen-activat... -

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Basic information

Entry
Database: PDB / ID: 2xlr
TitleJoint-functions of protein residues and NADP(H) in oxygen-activation by flavin-containing monooxygenase: Asn78Asp mutant
ComponentsFLAVIN-CONTAINING MONOOXYGENASE
KeywordsOXIDOREDUCTASE / TRIMETHYAMINURIA
Function / homology
Function and homology information


trimethylamine monooxygenase / N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding / identical protein 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 speciesMETHYLOPHAGA AMINISULFIDIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsOrru, R. / Fraaije, M.W. / Mattevi, A.
CitationJournal: J. Biol. Chem. / Year: 2010
Title: Joint functions of protein residues and NADP(H) in oxygen activation by flavin-containing monooxygenase.
Authors: Orru, R. / Pazmino, D.E. / Fraaije, M.W. / Mattevi, A.
History
DepositionJul 21, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: 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: FLAVIN-CONTAINING MONOOXYGENASE
B: FLAVIN-CONTAINING MONOOXYGENASE
C: FLAVIN-CONTAINING MONOOXYGENASE
D: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,48312
Polymers213,3674
Non-polymers6,1168
Water4,918273
1
B: FLAVIN-CONTAINING MONOOXYGENASE
C: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7416
Polymers106,6832
Non-polymers3,0584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-34.3 kcal/mol
Surface area32190 Å2
MethodPISA
2
A: FLAVIN-CONTAINING MONOOXYGENASE
D: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7416
Polymers106,6832
Non-polymers3,0584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-33.1 kcal/mol
Surface area31710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.059, 214.059, 152.811
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A5 - 501
2111B5 - 501
3111C5 - 501
4111D5 - 501

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Components

#1: Protein
FLAVIN-CONTAINING MONOOXYGENASE


Mass: 53341.738 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHYLOPHAGA AMINISULFIDIVORANS (bacteria)
Strain: SK1 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83XK4, EC: 1.14.13.8
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 73 TO ASP ENGINEERED RESIDUE IN CHAIN B, ASN 73 TO ASP ...ENGINEERED RESIDUE IN CHAIN A, ASN 73 TO ASP ENGINEERED RESIDUE IN CHAIN B, ASN 73 TO ASP ENGINEERED RESIDUE IN CHAIN C, ASN 73 TO ASP ENGINEERED RESIDUE IN CHAIN D, ASN 73 TO ASP

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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: 4.74 Å3/Da / Density % sol: 74.03 % / Description: NONE
Crystal growTemperature: 277 K / Method: microbatch / pH: 7.5
Details: CRYSTALS WERE OBTAINED USING MICROBATCH TECHNIQUE UNDER 100% PARAFFIN OIL AT 4 C BY MIXING EQUAL VOLUMES OF 8 MG PROTEIN/ML IN 25 MM TRIS/HCL PH 8.0, 250 MM NACL, 1 MM NADP (OR ANALOGUE), ...Details: CRYSTALS WERE OBTAINED USING MICROBATCH TECHNIQUE UNDER 100% PARAFFIN OIL AT 4 C BY MIXING EQUAL VOLUMES OF 8 MG PROTEIN/ML IN 25 MM TRIS/HCL PH 8.0, 250 MM NACL, 1 MM NADP (OR ANALOGUE), AND 20% (W/V) PEG4000 IN 100 MM NA/HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→54 Å / Num. obs: 129218 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.9
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VQ7

2vq7


Resolution: 2.55→53.51 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.86 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24423 6425 5 %RANDOM
Rwork0.2139 ---
obs0.2154 122681 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 41.762 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.55→53.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14671 0 404 273 15348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02215565
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.96321211
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85751788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3223.79781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.136152434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0821584
X-RAY DIFFRACTIONr_chiral_restr0.1310.22145
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112076
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9071.58933
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.862214404
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9236632
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7434.56807
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 3753 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.140.05
2Btight positional0.110.05
3Ctight positional0.150.05
4Dtight positional0.110.05
1Atight thermal0.340.5
2Btight thermal0.330.5
3Ctight thermal0.390.5
4Dtight thermal0.350.5
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 441 -
Rwork0.327 9021 -
obs--99.98 %

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