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- PDB-6jit: Complex structure of an imine reductase at 2.05 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 6jit
TitleComplex structure of an imine reductase at 2.05 Angstrom resolution
Components6-phosphogluconate dehydrogenase NAD-binding protein
KeywordsOXIDOREDUCTASE / imine reductases / highly active / stereoselective
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
1-(2-phenylethyl)-3,4-dihydroisoquinoline / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 6-phosphogluconate dehydrogenase NAD-binding protein
Similarity search - Component
Biological speciesStackebrandtia nassauensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.052 Å
AuthorsLi, H. / Wu, L. / Zheng, G.W. / Zhou, J.H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21878085 China
National Natural Science Foundation of China21536004 China
CitationJournal: To Be Published
Title: Complex structure of an imine reductase at 2.05 Angstrom resolution
Authors: Li, H. / Wu, L. / Zheng, G.W. / Zhou, J.H.
History
DepositionFeb 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: 6-phosphogluconate dehydrogenase NAD-binding protein
B: 6-phosphogluconate dehydrogenase NAD-binding protein
C: 6-phosphogluconate dehydrogenase NAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4066
Polymers93,3913
Non-polymers1,0143
Water10,809600
1
A: 6-phosphogluconate dehydrogenase NAD-binding protein
hetero molecules

A: 6-phosphogluconate dehydrogenase NAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3324
Polymers62,2612
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_444-y-1,-x-1,-z-1/31
Buried area8200 Å2
ΔGint-108 kcal/mol
Surface area21920 Å2
MethodPISA
2
B: 6-phosphogluconate dehydrogenase NAD-binding protein
C: 6-phosphogluconate dehydrogenase NAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2404
Polymers62,2612
Non-polymers9792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-88 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.598, 106.598, 168.343
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

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


Mass: 31130.479 Da / Num. of mol.: 3 / Mutation: T123I,F178L,G228A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stackebrandtia nassauensis (strain DSM 44728 / NRRL B-16338 / NBRC 102104 / LLR-40K-21) (bacteria)
Strain: DSM 44728 / NRRL B-16338 / NBRC 102104 / LLR-40K-21 / Gene: Snas_4330 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: D3Q3R0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-LW7 / 1-(2-phenylethyl)-3,4-dihydroisoquinoline


Mass: 235.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 5M ammonium acetate, 0.1M Tris-HCl pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 68583 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.234 / Net I/σ(I): 16.6
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 1.771

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JIZ

6jiz


Resolution: 2.052→47.951 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.92
RfactorNum. reflection% reflection
Rfree0.219 3320 4.88 %
Rwork0.1895 --
obs0.1909 68047 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.052→47.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6316 0 67 600 6983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036600
X-RAY DIFFRACTIONf_angle_d0.5679020
X-RAY DIFFRACTIONf_dihedral_angle_d15.7793947
X-RAY DIFFRACTIONf_chiral_restr0.0421074
X-RAY DIFFRACTIONf_plane_restr0.0041148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0517-2.0810.25241310.23372558X-RAY DIFFRACTION97
2.081-2.1120.2831370.22642653X-RAY DIFFRACTION98
2.112-2.1450.26051570.21792597X-RAY DIFFRACTION97
2.145-2.18020.28141340.22572644X-RAY DIFFRACTION97
2.1802-2.21780.29611550.24922692X-RAY DIFFRACTION99
2.2178-2.25810.53611220.44172604X-RAY DIFFRACTION97
2.2581-2.30160.33891330.31632646X-RAY DIFFRACTION98
2.3016-2.34850.28441350.2142689X-RAY DIFFRACTION100
2.3485-2.39960.25531270.20362744X-RAY DIFFRACTION100
2.3996-2.45540.27071220.19592700X-RAY DIFFRACTION100
2.4554-2.51680.23361510.20262693X-RAY DIFFRACTION100
2.5168-2.58490.22281520.20082710X-RAY DIFFRACTION100
2.5849-2.66090.23091560.19292696X-RAY DIFFRACTION100
2.6609-2.74680.23771430.19262695X-RAY DIFFRACTION100
2.7468-2.8450.2141280.1892712X-RAY DIFFRACTION100
2.845-2.95890.20921110.19582757X-RAY DIFFRACTION100
2.9589-3.09350.19271130.18292726X-RAY DIFFRACTION100
3.0935-3.25660.25681520.19352709X-RAY DIFFRACTION100
3.2566-3.46050.20841430.1812715X-RAY DIFFRACTION100
3.4605-3.72760.19351220.16812765X-RAY DIFFRACTION100
3.7276-4.10260.16911340.14672755X-RAY DIFFRACTION100
4.1026-4.69580.16481290.13232738X-RAY DIFFRACTION100
4.6958-5.91450.161480.16012762X-RAY DIFFRACTION100
5.9145-47.96390.1641850.15692767X-RAY DIFFRACTION99

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