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- PDB-9j5t: Imine Reductase from Burkholderia ubonensis in complex with NADH -

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Basic information

Entry
Database: PDB / ID: 9j5t
TitleImine Reductase from Burkholderia ubonensis in complex with NADH
Componentshypothetical protein WL01_04050
KeywordsOXIDOREDUCTASE / Imine reductase / Complex / NADH-dependent
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesBurkholderia ubonensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsMa, Z.F. / Shen, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Imine Reductase from Burkholderia ubonensis in complex with NADH
Authors: Ma, Z.F. / Shen, X.Y.
History
DepositionAug 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein WL01_04050
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5792
Polymers30,9161
Non-polymers6631
Water4,972276
1
A: hypothetical protein WL01_04050
hetero molecules

A: hypothetical protein WL01_04050
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1594
Polymers61,8322
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area10770 Å2
ΔGint-95 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.951, 69.951, 187.452
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

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Components

#1: Protein hypothetical protein WL01_04050


Mass: 30915.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ubonensis (bacteria) / Production host: Escherichia (bacteria)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG3350.Lithium sulphut,Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 0.979183 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Jan 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.43→93.73 Å / Num. obs: 94765 / % possible obs: 99.6 % / Redundancy: 13.8 % / Biso Wilson estimate: 9.17 Å2 / Rpim(I) all: 0.047 / Net I/σ(I): 9.8
Reflection shellResolution: 1.43→1.5 Å / Num. unique obs: 7071 / Rpim(I) all: 0.725

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→28.03 Å / SU ML: 0.1794 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4758
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2192 3726 3.93 %
Rwork0.1814 91039 -
obs0.1828 94765 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.93 Å2
Refinement stepCycle: LAST / Resolution: 1.43→28.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 44 276 2439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562202
X-RAY DIFFRACTIONf_angle_d1.01853001
X-RAY DIFFRACTIONf_chiral_restr0.0589353
X-RAY DIFFRACTIONf_plane_restr0.0053380
X-RAY DIFFRACTIONf_dihedral_angle_d5.2764314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.33171290.3013090X-RAY DIFFRACTION92.9
1.45-1.460.33241370.33237X-RAY DIFFRACTION95.26
1.46-1.480.31291380.27943320X-RAY DIFFRACTION97.77
1.48-1.510.29081410.26683348X-RAY DIFFRACTION99.23
1.51-1.530.28751400.25043416X-RAY DIFFRACTION100
1.53-1.550.31321390.22933393X-RAY DIFFRACTION100
1.55-1.580.27061420.21843373X-RAY DIFFRACTION99.91
1.58-1.60.27521370.20213373X-RAY DIFFRACTION100
1.6-1.630.22011420.1993398X-RAY DIFFRACTION99.97
1.63-1.670.23511390.1873450X-RAY DIFFRACTION100
1.67-1.70.25171380.18533355X-RAY DIFFRACTION100
1.7-1.740.251390.18123385X-RAY DIFFRACTION99.94
1.74-1.780.26711360.1793386X-RAY DIFFRACTION99.94
1.78-1.820.19821340.17733381X-RAY DIFFRACTION100
1.82-1.870.25311380.1753430X-RAY DIFFRACTION100
1.87-1.930.2411410.16943390X-RAY DIFFRACTION100
1.93-1.990.19521380.17233402X-RAY DIFFRACTION99.92
1.99-2.060.2431400.16473390X-RAY DIFFRACTION99.77
2.06-2.140.18281370.16883346X-RAY DIFFRACTION99.97
2.14-2.240.23021420.16553403X-RAY DIFFRACTION99.94
2.24-2.360.21461370.16383391X-RAY DIFFRACTION100
2.36-2.50.2081440.15943408X-RAY DIFFRACTION99.92
2.5-2.70.15671380.15573383X-RAY DIFFRACTION99.91
2.7-2.970.1661300.15453399X-RAY DIFFRACTION100
2.97-3.40.21991330.16113388X-RAY DIFFRACTION99.83
3.4-4.280.171390.15053401X-RAY DIFFRACTION100
4.28-28.030.1881380.19883403X-RAY DIFFRACTION99.89

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