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- PDB-8cp2: Structure of Aspartate-N-hydroxylase (FzmM)from Streptomyces sp. ... -

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Basic information

Entry
Database: PDB / ID: 8cp2
TitleStructure of Aspartate-N-hydroxylase (FzmM)from Streptomyces sp. V2: complex with NADPH and L-aspartate
ComponentsFAD-binding protein
KeywordsOXIDOREDUCTASE / Monooxygenase / flavin / aspartate
Function / homologyFAD-dependent urate hydroxylase HpyO, FAD/NAD(P)-binding domain / FAD-NAD(P)-binding / FAD/NAD(P)-binding domain superfamily / 3-NITROPROPANOIC ACID / ASPARTIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / FAD-binding protein
Function and homology information
Biological speciesStreptomyces sp. V2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRotilio, L. / Mattevi, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondazione CARIPLO2020-0894 Italy
CitationJournal: J.Biol.Chem. / Year: 2023
Title: A biosynthetic aspartate N-hydroxylase performs successive oxidations by holding intermediates at a site away from the catalytic center.
Authors: Rotilio, L. / Boverio, A. / Nguyen, Q.T. / Mannucci, B. / Fraaije, M.W. / Mattevi, A.
History
DepositionMar 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD-binding protein
B: FAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,96617
Polymers131,6612
Non-polymers4,30515
Water14,340796
1
A: FAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,15510
Polymers65,8301
Non-polymers2,3259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8117
Polymers65,8301
Non-polymers1,9806
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)244.591, 244.591, 128.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FAD-binding protein


Mass: 65830.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. V2 (bacteria) / Gene: DF268_28005 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RP+ / References: UniProt: A0A2V1NMV1

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Non-polymers , 7 types, 811 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-3NP / 3-NITROPROPANOIC ACID / Beta-Nitropropionic acid


Mass: 119.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5NO4 / Comment: inhibitor, agonist, toxin*YM
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 796 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 9% PEG 4000, 1.2 M di-Na tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.1→122.3 Å / Num. obs: 166781 / % possible obs: 100 % / Redundancy: 10.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.093 / Rrim(I) all: 0.301 / Χ2: 1.03 / Net I/σ(I): 7.4
Reflection shellResolution: 2.1→2.14 Å / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 1.8 / Num. measured all: 90751 / Num. unique obs: 8301 / CC1/2: 0.473 / Rpim(I) all: 0.736 / Rrim(I) all: 2.439 / Χ2: 0.99 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→122.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.007 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20207 8267 5 %RANDOM
Rwork0.17931 ---
obs0.18045 158494 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.891 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.36 Å20 Å2
2---0.72 Å20 Å2
3---2.33 Å2
Refinement stepCycle: 1 / Resolution: 2.1→122.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9279 0 285 796 10360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0139822
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179173
X-RAY DIFFRACTIONr_angle_refined_deg1.971.65613434
X-RAY DIFFRACTIONr_angle_other_deg1.3841.57820991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09251202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.99218.776588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71151414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.94415135
X-RAY DIFFRACTIONr_chiral_restr0.0870.21217
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022363
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_it3.1333.3014814
X-RAY DIFFRACTIONr_mcbond_other3.133.3014813
X-RAY DIFFRACTIONr_mcangle_it4.4574.9416011
X-RAY DIFFRACTIONr_mcangle_other4.4574.9426012
X-RAY DIFFRACTIONr_scbond_it4.7313.7825008
X-RAY DIFFRACTIONr_scbond_other4.733.7835009
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9125.4727423
X-RAY DIFFRACTIONr_long_range_B_refined8.42539.45410883
X-RAY DIFFRACTIONr_long_range_B_other8.42539.46110884
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 608 -
Rwork0.306 11694 -
obs--99.95 %

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