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- PDB-8kfk: Crystal Structure of Imine Reductase from Paenibacillus mucilaginosus -

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Basic information

Entry
Database: PDB / ID: 8kfk
TitleCrystal Structure of Imine Reductase from Paenibacillus mucilaginosus
Components6-phosphogluconate dehydrogenase
KeywordsOXIDOREDUCTASE / Imine Reductase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / 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 / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / DI(HYDROXYETHYL)ETHER / 6-phosphogluconate dehydrogenase
Similarity search - Component
Biological speciesPaenibacillus mucilaginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWu, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Crystal Structure of Imine Reductase from Paenibacillus mucilaginosus
Authors: Wu, K.
History
DepositionAug 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-phosphogluconate dehydrogenase
B: 6-phosphogluconate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5344
Polymers67,1042
Non-polymers4302
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-78 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.771, 133.771, 62.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein 6-phosphogluconate dehydrogenase


Mass: 33551.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus mucilaginosus (bacteria) / Gene: B2K_07400 / Production host: Escherichia coli (E. coli) / References: UniProt: I0BDU9
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.0 M Ammonium sulfate, 0.1 M Sodium acetate/Hydrochloric acid pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 42733 / % possible obs: 99.3 % / Redundancy: 10.18 % / Biso Wilson estimate: 28.78 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.051 / Net I/σ(I): 17.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 10.99 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1977 / CC1/2: 0.89 / Rpim(I) all: 0.281 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→28.21 Å / SU ML: 0.2716 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7375
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2403 2871 6.82 %
Rwork0.2072 39203 -
obs0.2095 42074 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4337 0 29 130 4496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00864455
X-RAY DIFFRACTIONf_angle_d1.06676042
X-RAY DIFFRACTIONf_chiral_restr0.0578687
X-RAY DIFFRACTIONf_plane_restr0.0058775
X-RAY DIFFRACTIONf_dihedral_angle_d19.65351612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.540.26351400.24011835X-RAY DIFFRACTION99.9
2.54-2.580.30041520.23491962X-RAY DIFFRACTION99.91
2.58-2.630.24551420.23261878X-RAY DIFFRACTION100
2.63-2.680.28481440.21121915X-RAY DIFFRACTION99.85
2.68-2.740.27641300.21641899X-RAY DIFFRACTION100
2.74-2.80.2861380.20961914X-RAY DIFFRACTION100
2.8-2.860.27131360.21381907X-RAY DIFFRACTION100
2.86-2.930.2671420.22621906X-RAY DIFFRACTION100
2.93-3.010.23681370.20281910X-RAY DIFFRACTION100
3.01-3.10.22281440.20321942X-RAY DIFFRACTION100
3.1-3.20.23261420.20831902X-RAY DIFFRACTION100
3.2-3.310.2691380.20971880X-RAY DIFFRACTION100
3.32-3.450.26271400.20581948X-RAY DIFFRACTION100
3.45-3.60.18451330.20721897X-RAY DIFFRACTION100
3.6-3.790.3739900.36371223X-RAY DIFFRACTION64.21
3.79-4.030.26561400.24421737X-RAY DIFFRACTION91.43
4.03-4.340.22121340.17431925X-RAY DIFFRACTION100
4.34-4.770.22611360.15861921X-RAY DIFFRACTION100
4.78-5.460.22481360.17251897X-RAY DIFFRACTION100
5.46-6.860.20991390.20751907X-RAY DIFFRACTION100
6.87-28.210.16931380.17141898X-RAY DIFFRACTION99.17

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