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- PDB-6smt: S-enantioselective imine reductase from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 6smt
TitleS-enantioselective imine reductase from Mycobacterium smegmatis
Components6-phosphogluconate dehydrogenase, NAD-binding
KeywordsOXIDOREDUCTASE / Imine reductase
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 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
(2S)-2-ethylhexan-1-ol / FORMIC ACID / Chem-NDP / DI(HYDROXYETHYL)ETHER / 6-phosphogluconate dehydrogenase, NAD-binding
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsMeyer, T. / Zumbraegel, N. / Geerds, C. / Groeger, H. / Niemann, H.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research031A184A Germany
CitationJournal: Biomolecules / Year: 2020
Title: Structural Characterization of an S -enantioselective Imine Reductase from Mycobacterium Smegmatis .
Authors: Meyer, T. / Zumbragel, N. / Geerds, C. / Groger, H. / Niemann, H.H.
History
DepositionAug 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: 6-phosphogluconate dehydrogenase, NAD-binding
B: 6-phosphogluconate dehydrogenase, NAD-binding
C: 6-phosphogluconate dehydrogenase, NAD-binding
D: 6-phosphogluconate dehydrogenase, NAD-binding
E: 6-phosphogluconate dehydrogenase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,67334
Polymers155,1745
Non-polymers5,49929
Water35,4901970
1
A: 6-phosphogluconate dehydrogenase, NAD-binding
B: 6-phosphogluconate dehydrogenase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,20512
Polymers62,0702
Non-polymers2,13610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12640 Å2
ΔGint-89 kcal/mol
Surface area20310 Å2
MethodPISA
2
C: 6-phosphogluconate dehydrogenase, NAD-binding
D: 6-phosphogluconate dehydrogenase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,20513
Polymers62,0702
Non-polymers2,13611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-91 kcal/mol
Surface area19540 Å2
MethodPISA
3
E: 6-phosphogluconate dehydrogenase, NAD-binding
hetero molecules

E: 6-phosphogluconate dehydrogenase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,52518
Polymers62,0702
Non-polymers2,45616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area12710 Å2
ΔGint-83 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.007, 77.023, 194.485
Angle α, β, γ (deg.)90.000, 90.200, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
6-phosphogluconate dehydrogenase, NAD-binding


Mass: 31034.783 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_6341 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0R5X0

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Non-polymers , 7 types, 1999 molecules

#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-2EH / (2S)-2-ethylhexan-1-ol


Mass: 130.228 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1970 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 20 % (w/v) PEG 3350, 0.2 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.55→100.42 Å / Num. obs: 248023 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 13.2 / Num. measured all: 1702995 / Scaling rejects: 6558
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.55-1.586.40.38476619118890.9280.1620.4173.296.3
8.49-100.4270.0871128516200.9870.0360.09430100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDS20180307data reduction
Aimless0.7.2data scaling
PHASER1.14rc3-3199phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G6R, 3ZGY, 4OQY, 4D3S

5g6r

3zgy

4oqy

4d3s


Resolution: 1.55→100.42 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.811 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1549 12250 4.9 %RANDOM
Rwork0.1308 ---
obs0.132 235772 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.91 Å2 / Biso mean: 18.425 Å2 / Biso min: 9.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å20.03 Å2
2---0.36 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 1.55→100.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10376 0 364 1970 12710
Biso mean--19.63 34.37 -
Num. residues----1432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01311589
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710690
X-RAY DIFFRACTIONr_angle_refined_deg2.2671.63815888
X-RAY DIFFRACTIONr_angle_other_deg1.7391.57824654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86951580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.73720.106568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.795151691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.28615113
X-RAY DIFFRACTIONr_chiral_restr0.1270.21594
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213673
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022526
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 872 -
Rwork0.173 17009 -
all-17881 -
obs--96.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (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)
10.1323-0.0238-0.20340.01460.00590.41780.027-0.02020.0227-0.01630.00650.00080.0010.0255-0.03350.0227-0.00550.00750.0047-0.00140.030543.613340.100842.4438
20.15670.0261-0.23030.16960.10740.4686-0.0060.00240.00380.02910.00470.00250.0382-0.00150.00130.0212-0.00410.00440.0048-0.00270.016228.593337.305566.1071
30.2716-0.06730.29890.098-0.03120.38220.03470.00250.04010.0011-0.0435-0.02840.0184-0.03160.00880.02610.00480.02380.0270.01980.031389.162317.025768.5749
40.2366-0.06110.34270.1679-0.1980.57610.0435-0.00450.0247-0.0722-0.06520.01630.11030.04390.02170.04320.03720.00580.04150.0010.015977.131613.046543.7417
50.498-0.01810.05330.0288-0.0380.0611-0.01810.0079-0.05060.0026-0.0032-0.0101-0.0074-0.01110.02130.0080.0006-0.00260.0306-0.01890.023944.2064-9.360695.3351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 288
2X-RAY DIFFRACTION2B3 - 291
3X-RAY DIFFRACTION3C4 - 288
4X-RAY DIFFRACTION4D3 - 288
5X-RAY DIFFRACTION5E3 - 288

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