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- PDB-5o98: Binary complex of Catharanthus roseus Vitrosamine Synthase with NADP+ -

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Basic information

Entry
Database: PDB / ID: 5o98
TitleBinary complex of Catharanthus roseus Vitrosamine Synthase with NADP+
ComponentsAlcohol dehydrogenase 1
KeywordsOXIDOREDUCTASE / Alkaloid / natural product / biosynthesis / short chain dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
short chain dehydrogenase / 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 / Alcohol dehydrogenase 1
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsStavrinides, A.K. / Tatsis, E.C. / Dang, T.T. / Caputi, L. / Stevenson, C.E.M. / Lawson, D.M. / Schneider, B. / O'Connor, S.E.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
European Research Council311363 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 (MET) United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N007905/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilDoctoral Training Partnership United Kingdom
CitationJournal: Chembiochem / Year: 2018
Title: Discovery of a Short-Chain Dehydrogenase from Catharanthus roseus that Produces a New Monoterpene Indole Alkaloid.
Authors: Stavrinides, A.K. / Tatsis, E.C. / Dang, T.T. / Caputi, L. / Stevenson, C.E.M. / Lawson, D.M. / Schneider, B. / O'Connor, S.E.
History
DepositionJun 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase 1
B: Alcohol dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5094
Polymers69,0222
Non-polymers1,4872
Water7,152397
1
A: Alcohol dehydrogenase 1
hetero molecules


  • defined by author&software
  • Evidence: light scattering, The protein sample was monodisperse with an estimated molecular size of 32 kDa, this being similar to the calculated molecular mass of 34,469 Da for the His-tagged ...Evidence: light scattering, The protein sample was monodisperse with an estimated molecular size of 32 kDa, this being similar to the calculated molecular mass of 34,469 Da for the His-tagged construct, gel filtration, The sample elution profile was consistent with a monomeric species.
  • 35.3 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)35,2552
Polymers34,5111
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alcohol dehydrogenase 1
hetero molecules


  • defined by author&software
  • Evidence: light scattering, The protein sample was monodisperse with an estimated molecular size of 32 kDa, this being similar to the calculated molecular mass of 34,469 Da for the His-tagged ...Evidence: light scattering, The protein sample was monodisperse with an estimated molecular size of 32 kDa, this being similar to the calculated molecular mass of 34,469 Da for the His-tagged construct, gel filtration, The sample elution profile was consistent with a monomeric species.
  • 35.3 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)35,2552
Polymers34,5111
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.830, 61.020, 162.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 7 - 299 / Label seq-ID: 25 - 317

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Alcohol dehydrogenase 1 /


Mass: 34511.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Native N-terminal MET is replaced by an affinity tag with the sequence MAHHHHHHSSGLEVLFQGP
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): solu / References: UniProt: A0A0C5DR25
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→55.3 Å / Num. obs: 85013 / % possible obs: 99.5 % / Redundancy: 9 % / Biso Wilson estimate: 28.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.024 / Rrim(I) all: 0.08 / Net I/σ(I): 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.55-1.594.71.120.6140.5491.25596.5
6.93-55.39.70.0950.9930.0320.199.9

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Processing

Software
NameVersionClassification
Aimless0.5.14data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O26

3o26


Resolution: 1.55→55.3 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.297 / SU ML: 0.06 / SU R Cruickshank DPI: 0.0754 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.074
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 4304 5.1 %RANDOM
Rwork0.169 ---
obs0.1701 80707 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 116.74 Å2 / Biso mean: 37.404 Å2 / Biso min: 20.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.62 Å20 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 1.55→55.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4292 0 96 409 4797
Biso mean--27.38 44.78 -
Num. residues----565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194559
X-RAY DIFFRACTIONr_bond_other_d0.0020.024254
X-RAY DIFFRACTIONr_angle_refined_deg1.4972.0066203
X-RAY DIFFRACTIONr_angle_other_deg0.9339890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4245579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30425.217184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56415777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4761519
X-RAY DIFFRACTIONr_chiral_restr0.0860.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02889
Refine LS restraints NCS

Ens-ID: 1 / Number: 17934 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 316 -
Rwork0.382 5688 -
all-6004 -
obs--96.2 %
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)
12.4702-1.37480.18323.1567-0.2931.674-0.0005-0.05410.15920.05740.0468-0.2168-0.04230.3604-0.04630.0189-0.0158-0.02640.1045-0.00250.0588-0.3908-14.858555.4928
23.03510.6898-2.63151.629-0.8755.29250.1025-0.52920.03740.2756-0.1020.0307-0.0450.5919-0.00050.0693-0.0131-0.03130.09910.00020.072-12.1984-14.795161.1049
31.907-0.1196-1.72591.06960.2053.6110.05850.140.10970.0848-0.02730.3279-0.1738-0.4057-0.03120.06810.0216-0.0020.06720.01660.153-23.3565-8.911154.9647
41.4967-0.24530.58852.0559-1.34795.3306-0.0136-0.0942-0.27490.04220.01040.25310.4628-0.30850.00330.1019-0.0280.00270.06520.01420.1459-16.3493-24.309352.9054
52.1761-0.08090.28622.52440.13923.14530.0731-0.3432-0.05910.3086-0.12840.16690.0637-0.36040.05540.0487-0.04730.01250.12220.00770.0189-45.5876-37.134373.5271
64.3172-0.27071.05211.9205-0.34142.40130.10180.0154-0.12090.0322-0.1404-0.27530.22330.14780.03870.05210.01480.00450.03180.03250.0552-34.4753-42.627564.4946
73.88791.45552.36883.47981.9076.06970.16650.339-0.2083-0.2398-0.0256-0.48180.26060.6127-0.14090.11220.12460.01790.20350.03340.2745-22.3343-47.883558.922
81.8221-0.18960.82071.67090.40933.50980.13580.16070.0941-0.1637-0.1691-0.1633-0.11890.18520.03330.02990.01740.01780.04660.03630.0337-37.6464-34.52359.2538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 80
2X-RAY DIFFRACTION2A81 - 123
3X-RAY DIFFRACTION3A124 - 246
4X-RAY DIFFRACTION4A247 - 299
5X-RAY DIFFRACTION5B7 - 121
6X-RAY DIFFRACTION6B122 - 177
7X-RAY DIFFRACTION7B178 - 220
8X-RAY DIFFRACTION8B221 - 299

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