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- PDB-8cp5: Structure of Aspartate-N-hydroxylase (FzmM)from Streptomyces sp. ... -

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Basic information

Entry
Database: PDB / ID: 8cp5
TitleStructure of Aspartate-N-hydroxylase (FzmM)from Streptomyces sp. V2: complex with NADPH and Sulphate
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 / nucleotide binding / 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: 2.54 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
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,18621
Polymers131,6612
Non-polymers4,52519
Water1,24369
1
A: FAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,43214
Polymers65,8301
Non-polymers2,60213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7547
Polymers65,8301
Non-polymers1,9236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)243.681, 243.681, 126.298
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 #1/H766 (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RP+ / References: UniProt: A0A2V1NMV1

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Non-polymers , 6 types, 88 molecules

#2: Chemical ChemComp-FAD / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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 / Details: 0.1 M Hepes pH 7 1.6 M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.54→80.98 Å / Num. obs: 91662 / % possible obs: 99.1 % / Redundancy: 10.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.061 / Rrim(I) all: 0.203 / Χ2: 0.99 / Net I/σ(I): 10.1 / Num. measured all: 993652
Reflection shellResolution: 2.54→2.58 Å / % possible obs: 86.4 % / Redundancy: 10.3 % / Rmerge(I) obs: 1.8 / Num. measured all: 40976 / Num. unique obs: 3985 / CC1/2: 0.293 / Rpim(I) all: 1.266 / Rrim(I) all: 4.151 / Χ2: 0.94 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→80.98 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.434 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24181 4503 4.9 %RANDOM
Rwork0.20423 ---
obs0.20603 87155 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.772 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0.57 Å20 Å2
2---1.14 Å20 Å2
3---3.71 Å2
Refinement stepCycle: 1 / Resolution: 2.54→80.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9271 0 284 69 9624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139809
X-RAY DIFFRACTIONr_bond_other_d0.0010.0149114
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.65413436
X-RAY DIFFRACTIONr_angle_other_deg1.31.57720853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.74351201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.33518.718585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.873151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.43515135
X-RAY DIFFRACTIONr_chiral_restr0.0750.21213
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211115
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_it3.9355.0344801
X-RAY DIFFRACTIONr_mcbond_other3.9345.0334799
X-RAY DIFFRACTIONr_mcangle_it5.5987.5586000
X-RAY DIFFRACTIONr_mcangle_other5.5987.5586000
X-RAY DIFFRACTIONr_scbond_it5.2245.575008
X-RAY DIFFRACTIONr_scbond_other5.0835.5464981
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.378.1267394
X-RAY DIFFRACTIONr_long_range_B_refined8.9258.12910251
X-RAY DIFFRACTIONr_long_range_B_other8.88458.12410247
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.54→2.605 Å
RfactorNum. reflection% reflection
Rfree0.51 330 -
Rwork0.531 5975 -
obs--92.18 %

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