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- PDB-4oqy: Streptomyces sp. GF3546 imine reductase -

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Basic information

Entry
Database: PDB / ID: 4oqy
TitleStreptomyces sp. GF3546 imine reductase
Components(S)-imine reductase
KeywordsOXIDOREDUCTASE / rossmann fold / imine reductase
Function / homology
Function and homology information


organic acid catabolic process / 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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily ...: / 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 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / 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
Chem-NDP / (S)-imine reductase
Similarity search - Component
Biological speciesStreptomyces sp. GF3546 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchneider, L.K. / Huber, T. / Gerhardt, S. / Muller, M. / Einsle, O.
CitationJournal: CHEMCATCHEM / Year: 2014
Title: Direct Reductive Amination of Ketones: Structure and Activity of S-Selective Imine Reductases from Streptomyces.
Authors: Huber, T. / Schneider, L. / Prag, A. / Gerhardt, S. / Einsle, O. / Muller, M.
History
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Other / Structure summary
Revision 1.2Nov 19, 2014Group: Other
Revision 1.3Aug 9, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: (S)-imine reductase
B: (S)-imine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6823
Polymers61,9362
Non-polymers7451
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-79 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.320, 68.240, 181.380
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: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 3 - 286 / Label seq-ID: 3 - 286

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

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Components

#1: Protein (S)-imine reductase


Mass: 30968.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. GF3546 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: M4ZS15
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.2 M (NH4)2SO4, 0.1 M BisTris, microseeding, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→54.59 Å / Num. all: 45000 / Num. obs: 44024 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→54.53 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.113 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24129 2198 5 %RANDOM
Rwork0.21643 ---
obs0.2177 41591 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.982 Å2
Baniso -1Baniso -2Baniso -3
1-4.86 Å2-0 Å2-0 Å2
2---0.43 Å20 Å2
3----4.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→54.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4064 0 48 152 4264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194200
X-RAY DIFFRACTIONr_bond_other_d0.0040.023985
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9775724
X-RAY DIFFRACTIONr_angle_other_deg1.05239190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2355538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85425.064156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07615670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.7871510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214710
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02884
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 15061 / 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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 160 -
Rwork0.304 3026 -
obs--96.49 %
Refinement TLS params.

S12: -0.0116 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (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)
10.72920.12390.85410.66610.21342.0247-0.0424-0.0392-0.03120.02890.0092-0.0069-0.05570.01350.00660.00250.0220.21280.00270.27047.172866.078714.4363
20.1246-0.0206-0.15040.17810.23971.67940.00320.0188-0.0263-0.00240.074-0.0106-0.1104-0.00080.02160.0015-0.00550.2338-0.00190.304611.214374.626551.9836
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 215
2X-RAY DIFFRACTION1B231 - 288
3X-RAY DIFFRACTION1A1000
4X-RAY DIFFRACTION2B3 - 218
5X-RAY DIFFRACTION2A232 - 286

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