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

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Basic information

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


trimethylamine monooxygenase / N,N-dimethylaniline monooxygenase activity / flavin adenine dinucleotide binding / NADP 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 / Chem-NA7 / DI(HYDROXYETHYL)ETHER / Trimethylamine monooxygenase
Similarity search - Component
Biological speciesMETHYLOPHAGA AMINISULFIDIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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. / 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 / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _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)220,11220
Polymers213,3634
Non-polymers6,74916
Water7,692427
1
B: FLAVIN-CONTAINING MONOOXYGENASE
C: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8189
Polymers106,6822
Non-polymers3,1367
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-18.1 kcal/mol
Surface area32040 Å2
MethodPISA
2
A: FLAVIN-CONTAINING MONOOXYGENASE
D: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,29411
Polymers106,6822
Non-polymers3,6139
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-20 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.679, 220.679, 130.531
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
1114A1 - 501
2114B1 - 501
3114C1 - 501
4114D1 - 501

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
FLAVIN-CONTAINING MONOOXYGENASE


Mass: 53340.754 Da / Num. of mol.: 4
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, 443 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-NA7 / [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE


Mass: 623.296 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24N5O16P3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 427 / 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: 4.3 Å3/Da / Density % sol: 71.4 % / 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 CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→42 Å / Num. obs: 110842 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

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

2vq7


Resolution: 2.6→41.15 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.875 / SU B: 9.192 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25188 5537 5 %RANDOM
Rwork0.20997 ---
obs0.21204 105293 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.502 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å2-0.78 Å20 Å2
2---1.57 Å20 Å2
3---2.35 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14620 0 440 427 15487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02215548
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0091.96321161
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24451778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22323.76782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.817152422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9041584
X-RAY DIFFRACTIONr_chiral_restr0.1360.22130
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112000
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_it0.7421.58882
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.456214324
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.31236666
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7274.56837
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: 3743 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.130.5
2Bmedium positional0.110.5
3Cmedium positional0.110.5
4Dmedium positional0.110.5
1Amedium thermal1.082
2Bmedium thermal0.992
3Cmedium thermal12
4Dmedium thermal0.882
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 358 -
Rwork0.327 7738 -
obs--99.99 %

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