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- PDB-6toe: Imine Reductase from Myxococcus stipitatus V8 variant in complex ... -

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Basic information

Entry
Database: PDB / ID: 6toe
TitleImine Reductase from Myxococcus stipitatus V8 variant in complex with NAD+
ComponentsCoenzyme F420-dependent NADP oxidoreductase
KeywordsOXIDOREDUCTASE / Imine / Amine / NADPH
Function / homology
Function and homology information


NADP binding / oxidoreductase activity
Similarity search - Function
: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Coenzyme F420-dependent NADP oxidoreductase
Similarity search - Component
Biological speciesMyxococcus stipitatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsSharma, M. / Nestl, B. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M006832/1 United Kingdom
CitationJournal: Chemcatchem / Year: 2021
Title: Inverting the Stereoselectivity of an NADH-Dependent Imine-Reductase Variant
Authors: Stockinger, P. / Borlinghaus, N. / Sharma, M. / Aberle, B. / Grogan, G. / Pleiss, J. / Nestl, B.
History
DepositionDec 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Coenzyme F420-dependent NADP oxidoreductase
B: Coenzyme F420-dependent NADP oxidoreductase
C: Coenzyme F420-dependent NADP oxidoreductase
D: Coenzyme F420-dependent NADP oxidoreductase
E: Coenzyme F420-dependent NADP oxidoreductase
F: Coenzyme F420-dependent NADP oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,29410
Polymers202,6406
Non-polymers2,6544
Water4,540252
1
A: Coenzyme F420-dependent NADP oxidoreductase
E: Coenzyme F420-dependent NADP oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2103
Polymers67,5472
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-97 kcal/mol
Surface area21820 Å2
MethodPISA
2
B: Coenzyme F420-dependent NADP oxidoreductase
F: Coenzyme F420-dependent NADP oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8744
Polymers67,5472
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-99 kcal/mol
Surface area22120 Å2
MethodPISA
3
C: Coenzyme F420-dependent NADP oxidoreductase
D: Coenzyme F420-dependent NADP oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2103
Polymers67,5472
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-93 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.412, 199.412, 97.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISLEULEUAA0 - 29020 - 310
21HISHISLEULEUBB0 - 29020 - 310
12HISHISLYSLYSAA0 - 29120 - 311
22HISHISLYSLYSCC0 - 29120 - 311
13HISHISLYSLYSAA0 - 29120 - 311
23HISHISLYSLYSDD0 - 29120 - 311
14METMETLYSLYSAA1 - 29121 - 311
24METMETLYSLYSEE1 - 29121 - 311
15METMETLEULEUAA1 - 29021 - 310
25METMETLEULEUFF1 - 29021 - 310
16HISHISLEULEUBB0 - 29020 - 310
26HISHISLEULEUCC0 - 29020 - 310
17HISHISLYSLYSBB0 - 29120 - 311
27HISHISLYSLYSDD0 - 29120 - 311
18METMETLYSLYSBB1 - 29121 - 311
28METMETLYSLYSEE1 - 29121 - 311
19METMETLEULEUBB1 - 29021 - 310
29METMETLEULEUFF1 - 29021 - 310
110HISHISLYSLYSCC0 - 29120 - 311
210HISHISLYSLYSDD0 - 29120 - 311
111METMETLYSLYSCC1 - 29121 - 311
211METMETLYSLYSEE1 - 29121 - 311
112METMETLEULEUCC1 - 29021 - 310
212METMETLEULEUFF1 - 29021 - 310
113METMETLYSLYSDD1 - 29121 - 311
213METMETLYSLYSEE1 - 29121 - 311
114METMETLYSLYSDD1 - 29121 - 311
214METMETLYSLYSFF1 - 29121 - 311
115METMETLYSLYSEE1 - 29121 - 311
215METMETLYSLYSFF1 - 29121 - 311

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Coenzyme F420-dependent NADP oxidoreductase / Imine reductase


Mass: 33773.398 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus stipitatus (bacteria) / Gene: MYSTI_01767 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L7U9F5
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES pH 7.0; 20% (w/v) PEG 6K; o.2 M ammonium choride

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.78→48.97 Å / Num. obs: 55975 / % possible obs: 100 % / Redundancy: 20.4 % / Biso Wilson estimate: 35 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.05 / Net I/σ(I): 16.1
Reflection shellResolution: 2.78→2.86 Å / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 4 / Num. unique obs: 4545 / CC1/2: 0.91 / Rpim(I) all: 0.29

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OCM

5ocm


Resolution: 2.78→47.94 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.475 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 9.882 / ESU R Free: 0.322
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 2844 5.1 %RANDOM
Rwork0.1918 ---
obs0.1937 53100 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.31 Å2 / Biso mean: 44.497 Å2 / Biso min: 19.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å2-0 Å2
2---0.34 Å20 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 2.78→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12822 0 158 252 13232
Biso mean--60.3 38.16 -
Num. residues----1743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01313233
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712264
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.63118049
X-RAY DIFFRACTIONr_angle_other_deg1.3321.5728148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36851741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69421.986589
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.844152021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6831578
X-RAY DIFFRACTIONr_chiral_restr0.0740.21857
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215111
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022736
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A86130.08
12B86130.08
21A85050.08
22C85050.08
31A78010.11
32D78010.11
41A82150.11
42E82150.11
51A83560.11
52F83560.11
61B85690.05
62C85690.05
71B78590.1
72D78590.1
81B82470.11
82E82470.11
91B83310.1
92F83310.1
101C78080.1
102D78080.1
111C81580.11
112E81580.11
121C82110.1
122F82110.1
131D80240.08
132E80240.08
141D80800.08
142F80800.08
151E85450.07
152F85450.07
LS refinement shellResolution: 2.78→2.852 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 231 -
Rwork0.255 3897 -
all-4128 -
obs--100 %

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