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- PDB-6to4: Imine Reductase from Myxococcus stipitatus in complex with NADP+ -

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Basic information

Entry
Database: PDB / ID: 6to4
TitleImine Reductase from Myxococcus stipitatus in complex with NADP+
ComponentsCoenzyme F420-dependent NADP oxidoreductase
KeywordsOXIDOREDUCTASE / Imine / Amine / NADPH
Function / homology3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NADP binding / oxidoreductase activity / NAD(P)-binding domain superfamily / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Coenzyme F420-dependent NADP oxidoreductase
Function and homology information
Biological speciesMyxococcus stipitatus DSM 14675 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,3387
Polymers126,1084
Non-polymers2,2303
Water2,738152
1
A: Coenzyme F420-dependent NADP oxidoreductase
D: Coenzyme F420-dependent NADP oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7973
Polymers63,0542
Non-polymers7431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10140 Å2
ΔGint-92 kcal/mol
Surface area21750 Å2
MethodPISA
2
B: Coenzyme F420-dependent NADP oxidoreductase
C: Coenzyme F420-dependent NADP oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5414
Polymers63,0542
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-96 kcal/mol
Surface area20890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.707, 42.584, 121.404
Angle α, β, γ (deg.)90.000, 110.370, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUAA3 - 2903 - 290
21PROPROLEULEUBB3 - 2903 - 290
12LYSLYSLEULEUAA2 - 2902 - 290
22LYSLYSLEULEUCC2 - 2902 - 290
13THRTHRLYSLYSAA6 - 2916 - 291
23THRTHRLYSLYSDD6 - 2916 - 291
14PROPROLEULEUBB3 - 2903 - 290
24PROPROLEULEUCC3 - 2903 - 290
15THRTHRLYSLYSBB6 - 2916 - 291
25THRTHRLYSLYSDD6 - 2916 - 291
16THRTHRLYSLYSCC6 - 2916 - 291
26THRTHRLYSLYSDD6 - 2916 - 291

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Coenzyme F420-dependent NADP oxidoreductase


Mass: 31526.998 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus stipitatus DSM 14675 (bacteria)
Gene: MYSTI_01767 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L7U9F5
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris-HCl pH 8.5; 300 mM NaCl; 0.2 M ammonium acetate; 25% (w/v) PEG 3350; 5 mM NADP+

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.29→49.32 Å / Num. obs: 52197 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 40 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.03 / Net I/σ(I): 20.9
Reflection shellResolution: 2.29→2.36 Å / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4505 / CC1/2: 0.93 / Rpim(I) all: 0.28

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OCM

5ocm


Resolution: 2.29→49.32 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.624 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.232
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 2520 4.8 %RANDOM
Rwork0.2117 ---
obs0.2131 49666 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.89 Å2 / Biso mean: 51.36 Å2 / Biso min: 26.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å2-0 Å21.72 Å2
2--2.3 Å2-0 Å2
3----1.92 Å2
Refinement stepCycle: final / Resolution: 2.29→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8287 0 144 152 8583
Biso mean--43.19 43.62 -
Num. residues----1146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0158556
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177658
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.7611669
X-RAY DIFFRACTIONr_angle_other_deg0.4821.75717696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62851134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74821.854356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.901151270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6621550
X-RAY DIFFRACTIONr_chiral_restr0.0590.21217
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029730
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021581
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A83410.09
12B83410.09
21A85430.08
22C85430.08
31A73740.08
32D73740.08
41B83760.08
42C83760.08
51B73760.09
52D73760.09
61C74140.08
62D74140.08
LS refinement shellResolution: 2.29→2.349 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 206 -
Rwork0.276 3642 -
all-3848 -
obs--100 %

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