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- PDB-4d3s: Imine reductase from Nocardiopsis halophila -

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Basic information

Entry
Database: PDB / ID: 4d3s
TitleImine reductase from Nocardiopsis halophila
ComponentsIMINE REDUCTASE
KeywordsOXIDOREDUCTASE / NADPH
Function / homology
Function and homology information


organic acid catabolic process / dihydrofolate reductase / dihydrofolate reductase activity / NADP 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 / 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
Biological speciesNOCARDIOPSIS HALOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsMan, H. / Hart, S. / Turkenburg, J.P. / Grogan, G.
CitationJournal: Chembiochem / Year: 2015
Title: Structure, Activity and Stereoselectivity of Nadph-Dependent Oxidoreductases Catalysing the S-Selective Reduction of the Imine Substrate 2-Methylpyrroline.
Authors: Man, H. / Wells, E. / Hussain, S. / Leipold, F. / Hart, S. / Turkenburg, J.P. / Turner, N.J. / Grogan, G.
History
DepositionOct 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: IMINE REDUCTASE
D: IMINE REDUCTASE
E: IMINE REDUCTASE
F: IMINE REDUCTASE
G: IMINE REDUCTASE
H: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,64610
Polymers246,0618
Non-polymers5852
Water9,134507
1
D: IMINE REDUCTASE
E: IMINE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)61,5152
Polymers61,5152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-79.2 kcal/mol
Surface area20970 Å2
MethodPISA
2
C: IMINE REDUCTASE
F: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8083
Polymers61,5152
Non-polymers2921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-75.9 kcal/mol
Surface area20620 Å2
MethodPISA
3
A: IMINE REDUCTASE
H: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8083
Polymers61,5152
Non-polymers2921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-76.3 kcal/mol
Surface area20890 Å2
MethodPISA
4
B: IMINE REDUCTASE
G: IMINE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)61,5152
Polymers61,5152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-75.5 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.170, 153.920, 105.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.89, -0.1833, 0.4174), (0.05344, 0.9512, 0.3038), (-0.4527, -0.2481, 0.8564)-16.52, 3.958, 117.5
2given(-0.9978, 0.04962, 0.04502), (-0.04934, -0.9988, 0.007277), (0.04532, 0.00504, 0.999)137.7, 79.55, 49.97
3given(-0.8935, -0.1783, -0.4121), (-0.04142, 0.9466, -0.3197), (0.4471, -0.2686, -0.8532)238.9, 63.52, 157.6
4given(-0.4849, 0.5193, 0.7037), (-0.3633, -0.8515, 0.3781), (0.7956, -0.07229, 0.6015)58.31, 68.89, -40.04
5given(-0.1062, -0.2705, -0.9568), (-0.31, 0.9233, -0.2266), (0.9448, 0.2726, -0.1819)160.6, 49.62, 65.75
6given(0.4809, 0.4922, -0.7256), (0.3458, -0.867, -0.3589), (-0.8057, -0.07833, -0.5872)68.97, 52.11, 225
7given(0.07172, 0.2796, -0.9574), (0.3303, -0.9124, -0.2417), (-0.9411, -0.2989, -0.1578)177.3, 88.36, 228.7

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Components

#1: Protein
IMINE REDUCTASE


Mass: 30757.660 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NOCARDIOPSIS HALOPHILA (bacteria) / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0J9X1X6*PLUS, dihydrofolate reductase
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsN-OCTYL-BETA-D-GLUCOPYRANOSIDE: CRYSTALLISATION ADDITIVE

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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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 5.5
Details: 18% (W/V) PEG 3350; 0. 2 M MGCL2; 0.1M BIS-TRIS PROPANE PH 5.5; 1% (W/V) N-OCTYL-BETA-D-OCTYLPYRANOSIDE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: May 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.39→67.57 Å / Num. obs: 94683 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1
Reflection shellResolution: 2.39→2.47 Å / Redundancy: 7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZGY

3zgy


Resolution: 2.24→67.57 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.948 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26577 5458 4.9 %RANDOM
Rwork0.2302 ---
obs0.23199 94683 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.319 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--2.03 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.24→67.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15838 0 40 507 16385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01916198
X-RAY DIFFRACTIONr_bond_other_d0.010.0214947
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.96522063
X-RAY DIFFRACTIONr_angle_other_deg1.8813.00234145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02952216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59523.172580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.631152203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9861596
X-RAY DIFFRACTIONr_chiral_restr0.0980.22574
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02118832
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023572
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_it4.0535.0078917
X-RAY DIFFRACTIONr_mcbond_other4.0535.0078916
X-RAY DIFFRACTIONr_mcangle_it5.9587.49311114
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1945.0037281
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
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 418 -
Rwork0.326 7692 -
obs--99.98 %

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