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- PDB-5fwn: Imine Reductase from Amycolatopsis orientalis. Closed form in in ... -

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Basic information

Entry
Database: PDB / ID: 5fwn
TitleImine Reductase from Amycolatopsis orientalis. Closed form in in complex with (R)- Methyltetrahydroisoquinoline
ComponentsIMINE REDUCTASE
KeywordsOXIDOREDUCTASE / IMINE / AMINE / NADPH
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / nucleosome binding / NADP binding / oxidoreductase activity / chromatin / DNA binding / metal ion binding
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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding Rossmann-like Domain ...: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / (1R)-1-methyl-1,2,3,4-tetrahydroisoquinoline / Putative dehydrogenase
Similarity search - Component
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsMan, H. / Aleku, G. / Turner, N.J. / Grogan, G.
CitationJournal: Acs Catalysis / Year: 2016
Title: Stereoselectivity and Structural Characterization of an Imine Reductase (Ired) from Amycolatopsis Orientalis
Authors: Aleku, G.A. / Man, H. / France, S.P. / Leipold, F. / Hussain, S. / Toca-Gonzalez, L. / Marchington, R. / Hart, S. / Turkenburg, J.P. / Grogan, G. / Turner, N.J.
History
DepositionFeb 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMINE REDUCTASE
B: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2568
Polymers60,9812
Non-polymers1,2756
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9990 Å2
ΔGint-143.8 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.852, 65.671, 147.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 5 - 290 / Label seq-ID: 5 - 290

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

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Components

#1: Protein IMINE REDUCTASE


Mass: 30490.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: R4SNK4, EC: 1.5.1.48
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-YLG / (1R)-1-methyl-1,2,3,4-tetrahydroisoquinoline


Mass: 147.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.13 Å3/Da / Density % sol: 42.4 % / Description: NONE
Crystal growpH: 8
Details: 0.25 M LI2SO4, 0.1 M BISTRIS PH 6.5, 23% W/V PEG 3350, 1 MM NADPH AND 1 MM RAC-AMINE.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.14→73.78 Å / Num. obs: 29186 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.3
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A9R

5a9r


Resolution: 2.14→73.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.053 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22377 1426 4.9 %RANDOM
Rwork0.17132 ---
obs0.17401 27700 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.14→73.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4071 0 62 213 4346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194229
X-RAY DIFFRACTIONr_bond_other_d0.0070.023997
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.9865791
X-RAY DIFFRACTIONr_angle_other_deg1.5013.0019160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46424.178146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57815603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5011518
X-RAY DIFFRACTIONr_chiral_restr0.1050.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214816
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02889
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3362.7072257
X-RAY DIFFRACTIONr_mcbond_other2.3292.7062256
X-RAY DIFFRACTIONr_mcangle_it3.3454.0422814
X-RAY DIFFRACTIONr_mcangle_other3.3454.0422815
X-RAY DIFFRACTIONr_scbond_it3.1483.111972
X-RAY DIFFRACTIONr_scbond_other3.113.091957
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.554.532951
X-RAY DIFFRACTIONr_long_range_B_refined6.81123.0244900
X-RAY DIFFRACTIONr_long_range_B_other6.8123.0314901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 28078 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.14→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 94 -
Rwork0.188 2037 -
obs--100 %

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