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- PDB-5feu: Noroxomaritidine/Norcraugsodine Reductase in complex with NADP+ -

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Basic information

Entry
Database: PDB / ID: 5feu
TitleNoroxomaritidine/Norcraugsodine Reductase in complex with NADP+
ComponentsNoroxomaritidine/Norcraugsodine Reductase
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase/reductase alkaloid biosynthesis
Function / homology
Function and homology information


alkaloid metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleotide binding
Similarity search - Function
Tropinone reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Noroxomaritidine/norcraugsodine reductase
Similarity search - Component
Biological speciesNarcissus pseudonarcissus (daffodil)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsHolland, C. / Jez, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1RC2GM092561 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Identification of a Noroxomaritidine Reductase with Amaryllidaceae Alkaloid Biosynthesis Related Activities.
Authors: Kilgore, M.B. / Holland, C.K. / Jez, J.M. / Kutchan, T.M.
History
DepositionDec 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Noroxomaritidine/Norcraugsodine Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9312
Polymers31,1871
Non-polymers7431
Water2,468137
1
A: Noroxomaritidine/Norcraugsodine Reductase
hetero molecules

A: Noroxomaritidine/Norcraugsodine Reductase
hetero molecules

A: Noroxomaritidine/Norcraugsodine Reductase
hetero molecules

A: Noroxomaritidine/Norcraugsodine Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,7238
Polymers124,7494
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z+1/21
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area18850 Å2
ΔGint-119 kcal/mol
Surface area32300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.377, 60.377, 136.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

21A-509-

HOH

31A-532-

HOH

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Components

#1: Protein Noroxomaritidine/Norcraugsodine Reductase


Mass: 31187.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Narcissus pseudonarcissus (daffodil) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1A9TAK5*PLUS
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG-8000 100 mM HEPES buffer (pH 7.5).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.73→45.2 Å / Num. obs: 27021 / % possible obs: 99.7 % / Redundancy: 13.6 % / Rsym value: 0.106 / Net I/σ(I): 22
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.4 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data collection
SCALEPACKdata scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AE2

2ae2


Resolution: 1.73→45.169 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.81 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2106 1359 5.03 %
Rwork0.1786 --
obs0.1801 27018 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→45.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 48 137 2033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061968
X-RAY DIFFRACTIONf_angle_d1.0322688
X-RAY DIFFRACTIONf_dihedral_angle_d14.126726
X-RAY DIFFRACTIONf_chiral_restr0.042311
X-RAY DIFFRACTIONf_plane_restr0.005343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7299-1.79180.29371150.23062474X-RAY DIFFRACTION98
1.7918-1.86350.27691100.21412515X-RAY DIFFRACTION99
1.8635-1.94830.24161570.19742521X-RAY DIFFRACTION99
1.9483-2.0510.19231450.17722490X-RAY DIFFRACTION100
2.051-2.17950.23781380.17442541X-RAY DIFFRACTION99
2.1795-2.34780.22351410.17532530X-RAY DIFFRACTION100
2.3478-2.58410.24921310.18172572X-RAY DIFFRACTION100
2.5841-2.95790.22761470.19032584X-RAY DIFFRACTION100
2.9579-3.72640.18431520.18132620X-RAY DIFFRACTION100
3.7264-45.18470.1871230.16312812X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.66840.4494-0.64451.54260.81530.9136-0.03420.02640.22890.02050.0625-0.2742-0.92910.8721-0.02940.5148-0.2968-0.01810.56080.0640.32319.505319.283723.732
21.64340.1908-0.10371.51040.48610.21920.03570.40160.5067-0.3653-0.0397-0.0454-1.55150.6672-0.08680.8592-0.4267-0.00560.58030.16270.403216.33123.367310.08
36.51481.83341.30961.95360.11910.3104-0.09270.6794-0.135-0.48970.1183-0.29-0.47311.38590.03280.3565-0.14470.01780.9220.03120.240218.41259.44054.6007
40.24550.4729-0.11470.93090.30042.8189-0.0350.0984-0.0371-0.0498-0.0108-0.0455-0.27520.36630.05040.1618-0.0156-0.01190.23060.02060.21086.17946.439416.9353
53.3052-1.0407-1.22992.77270.96254.2452-0.07580.09660.25430.04540.06080.0864-0.78790.05660.02160.3192-0.0674-0.04940.21050.04810.22494.139214.350326.6691
65.112-1.5837-0.25291.90730.11922.6705-0.0404-0.05240.080.0320.06090.0039-0.5210.46560.00070.2836-0.1046-0.03090.25070.01540.19249.551112.680731.1234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 99 )
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 192 )
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 237 )
6X-RAY DIFFRACTION6chain 'A' and (resid 238 through 271 )

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