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- PDB-8a3x: Imine Reductase from Ensifer adhaerens in complex with NADP+ -

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Basic information

Entry
Database: PDB / ID: 8a3x
TitleImine Reductase from Ensifer adhaerens in complex with NADP+
ComponentsNAD_binding_2 domain-containing protein
KeywordsOXIDOREDUCTASE / Imine Reductase / IRED / NADP+ / amine
Function / homology
Function and homology information


NADP binding / oxidoreductase activity
Similarity search - Function
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
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 6-phosphogluconate dehydrogenase NADP-binding domain-containing protein
Similarity search - Component
Biological speciesEnsifer adhaerens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsGilio, A.K. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2023
Title: A Reductive Aminase Switches to Imine Reductase Mode for a Bulky Amine Substrate.
Authors: Gilio, A.K. / Thorpe, T.W. / Heyam, A. / Petchey, M.R. / Pogranyi, B. / France, S.P. / Howard, R.M. / Karmilowicz, M.J. / Lewis, R. / Turner, N. / Grogan, G.
History
DepositionJun 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 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: NAD_binding_2 domain-containing protein
B: NAD_binding_2 domain-containing protein
C: NAD_binding_2 domain-containing protein
D: NAD_binding_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,55112
Polymers124,4214
Non-polymers3,1308
Water64936
1
A: NAD_binding_2 domain-containing protein
B: NAD_binding_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7756
Polymers62,2102
Non-polymers1,5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-96 kcal/mol
Surface area21260 Å2
MethodPISA
2
C: NAD_binding_2 domain-containing protein
D: NAD_binding_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7756
Polymers62,2102
Non-polymers1,5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-96 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.959, 57.535, 116.441
Angle α, β, γ (deg.)90.000, 94.960, 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: _ / 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
11PROPROLYSLYSAA3 - 2923 - 292
21PROPROLYSLYSBB3 - 2923 - 292
12METMETLYSLYSAA1 - 2921 - 292
22METMETLYSLYSCC1 - 2921 - 292
13METMETLYSLYSAA1 - 2921 - 292
23METMETLYSLYSDD1 - 2921 - 292
14PROPROLYSLYSBB3 - 2923 - 292
24PROPROLYSLYSCC3 - 2923 - 292
15PROPROLYSLYSBB3 - 2923 - 292
25PROPROLYSLYSDD3 - 2923 - 292
16METMETALAALACC1 - 2931 - 293
26METMETALAALADD1 - 2931 - 293

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
NAD_binding_2 domain-containing protein


Mass: 31105.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ensifer adhaerens (bacteria) / Gene: AC244_29830 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8BGL4
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 30% (w/v) PEG 2000 MME; 0.2 M KSCN; protein at 50 mg mL-1
Temp details: Grown at 6 deg C

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.58→58 Å / Num. obs: 38177 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 31 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.15 / Net I/σ(I): 4.4
Reflection shellResolution: 2.58→2.69 Å / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4621 / CC1/2: 0.67 / Rpim(I) all: 0.97

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OCM

5ocm


Resolution: 2.58→58 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.905 / SU B: 24.897 / SU ML: 0.452 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.714 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2808 1892 5 %RANDOM
Rwork0.2357 ---
obs0.238 36273 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.07 Å2 / Biso mean: 52.967 Å2 / Biso min: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å28.45 Å2
2---3.75 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 2.58→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8524 0 196 37 8757
Biso mean--49.99 33.55 -
Num. residues----1172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138912
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158354
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.63512182
X-RAY DIFFRACTIONr_angle_other_deg1.2581.57219086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66351174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22520.542406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.669151281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3851571
X-RAY DIFFRACTIONr_chiral_restr0.0630.21239
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022032
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A86880.06
12B86880.06
21A87470.07
22C87470.07
31A87770.07
32D87770.07
41B86080.06
42C86080.06
51B86360.06
52D86360.06
61C87680.06
62D87680.06
LS refinement shellResolution: 2.58→2.647 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 135 -
Rwork0.354 2675 -
all-2810 -
obs--99.89 %

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