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

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Basic information

Entry
Database: PDB / ID: 2xlp
TitleJoint-functions of protein residues and NADP(H) in oxygen-activation by flavin-containing monooxygenase: Asn78Ser 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 / DI(HYDROXYETHYL)ETHER / Trimethylamine monooxygenase
Similarity search - Component
Biological speciesMETHYLOPHAGA AMINISULFIDIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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)220,85521
Polymers213,2554
Non-polymers7,60017
Water1,72996
1
A: FLAVIN-CONTAINING MONOOXYGENASE
D: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,37410
Polymers106,6272
Non-polymers3,7478
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-30.7 kcal/mol
Surface area32230 Å2
MethodPISA
2
B: FLAVIN-CONTAINING MONOOXYGENASE
C: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,48011
Polymers106,6272
Non-polymers3,8539
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-29.3 kcal/mol
Surface area31760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.708, 219.708, 131.441
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
1111A1 - 501
2111B1 - 501
3111C1 - 501
4111D1 - 501

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
FLAVIN-CONTAINING MONOOXYGENASE


Mass: 53313.730 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

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Non-polymers , 5 types, 113 molecules

#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: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 73 TO SER ENGINEERED RESIDUE IN CHAIN B, ASN 73 TO SER ...ENGINEERED RESIDUE IN CHAIN A, ASN 73 TO SER ENGINEERED RESIDUE IN CHAIN B, ASN 73 TO SER ENGINEERED RESIDUE IN CHAIN C, ASN 73 TO SER ENGINEERED RESIDUE IN CHAIN D, ASN 73 TO SER

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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: 4.29 Å3/Da / Density % sol: 71.35 % / 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: ID14-3 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→62.12 Å / Num. obs: 88448 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0078refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VQ7

2vq7


Resolution: 2.8→62.12 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.615 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21376 4410 5 %RANDOM
Rwork0.19304 ---
obs0.19407 83923 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.415 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å2-0.81 Å20 Å2
2---1.62 Å20 Å2
3---2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.8→62.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14614 0 499 96 15209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02215600
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.96721243
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36551778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69623.744780
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.487152420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7661584
X-RAY DIFFRACTIONr_chiral_restr0.1150.22134
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112040
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_it0.6781.58882
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.424214324
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.08836718
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5774.56919
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: 3750 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.070.05
2Btight positional0.070.05
3Ctight positional0.050.05
4Dtight positional0.050.05
1Atight thermal0.10.5
2Btight thermal0.10.5
3Ctight thermal0.10.5
4Dtight thermal0.10.5
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 329 -
Rwork0.307 6064 -
obs--97.86 %

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