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- PDB-8whg: imine reductase mutant - M3 -

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Basic information

Entry
Database: PDB / ID: 8whg
Titleimine reductase mutant - M3
Components6-phosphogluconate dehydrogenase NAD-binding protein
KeywordsOXIDOREDUCTASE / imine reductase / mutant / Streptomyces viridochromogenes
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / nucleosome binding / NADP binding / oxidoreductase activity / chromatin / DNA 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 6-phosphogluconate dehydrogenase NAD-binding protein
Similarity search - Component
Biological speciesStreptomyces viridochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsZhu, X.X. / Chen, X.R. / Zheng, G.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A structure of imine reductase mutant at 2.7 Angstroms resolution.
Authors: Zhu, X.X. / Chen, X.R. / Zheng, G.W.
History
DepositionSep 23, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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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 protein
B: 6-phosphogluconate dehydrogenase NAD-binding protein
C: 6-phosphogluconate dehydrogenase NAD-binding protein
D: 6-phosphogluconate dehydrogenase NAD-binding protein
E: 6-phosphogluconate dehydrogenase NAD-binding protein
F: 6-phosphogluconate dehydrogenase NAD-binding protein
G: 6-phosphogluconate dehydrogenase NAD-binding protein
H: 6-phosphogluconate dehydrogenase NAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,67210
Polymers248,1858
Non-polymers1,4872
Water4,252236
1
A: 6-phosphogluconate dehydrogenase NAD-binding protein
C: 6-phosphogluconate dehydrogenase NAD-binding protein


Theoretical massNumber of molelcules
Total (without water)62,0462
Polymers62,0462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint-90 kcal/mol
Surface area21060 Å2
MethodPISA
2
B: 6-phosphogluconate dehydrogenase NAD-binding protein
D: 6-phosphogluconate dehydrogenase NAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7903
Polymers62,0462
Non-polymers7431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-92 kcal/mol
Surface area20730 Å2
MethodPISA
3
E: 6-phosphogluconate dehydrogenase NAD-binding protein
F: 6-phosphogluconate dehydrogenase NAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7903
Polymers62,0462
Non-polymers7431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-97 kcal/mol
Surface area20830 Å2
MethodPISA
4
G: 6-phosphogluconate dehydrogenase NAD-binding protein
H: 6-phosphogluconate dehydrogenase NAD-binding protein


Theoretical massNumber of molelcules
Total (without water)62,0462
Polymers62,0462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-82 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)335.102, 96.071, 103.790
Angle α, β, γ (deg.)90.00, 100.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-406-

HOH

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Components

#1: Protein
6-phosphogluconate dehydrogenase NAD-binding protein / Imine reductase


Mass: 31023.113 Da / Num. of mol.: 8
Mutation: T40R,T73S,L97Y,A126G,I127P,D130W,I131L,A135R,V137I,M214L,V217L,Y221R
Source method: isolated from a genetically manipulated source
Details: Sequence reference for strain Streptomyces viridochromogenes is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id D9X416. Author stated: Due ...Details: Sequence reference for strain Streptomyces viridochromogenes is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id D9X416. Author stated: Due to a octemer in the crystal cell, and two dimer among them were explicitly match with electron cloud density. While these missing residues in H chain can't perfectly match with corresponding electron cloud, we decide to remove them. Because other right chains has been solved, the H chain is not focused.
Source: (gene. exp.) Streptomyces viridochromogenes (bacteria)
Gene: SSQG_04344
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D9X416
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG3350,sodium chloride, Bis-Tris

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.71→102.08 Å / Num. obs: 87190 / % possible obs: 98.9 % / Redundancy: 6.4 % / CC1/2: 0.985 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.06 / Rrim(I) all: 0.152 / Χ2: 0.9 / Net I/σ(I): 7.2 / Num. measured all: 558118
Reflection shellResolution: 2.71→2.78 Å / % possible obs: 98.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.665 / Num. measured all: 32908 / Num. unique obs: 6360 / CC1/2: 0.674 / Rpim(I) all: 0.32 / Rrim(I) all: 0.741 / Χ2: 0.87 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSV2023data scaling
XDSV2023data reduction
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→102.06 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2709 1929 2.3 %
Rwork0.2298 --
obs0.2308 83887 94.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→102.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15984 0 96 236 16316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d6.5812352
X-RAY DIFFRACTIONf_chiral_restr0.0342619
X-RAY DIFFRACTIONf_plane_restr0.0032879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.780.37191240.31295156X-RAY DIFFRACTION84
2.78-2.850.36761220.29675379X-RAY DIFFRACTION88
2.85-2.940.34591330.28275593X-RAY DIFFRACTION91
2.94-3.030.33751330.27065694X-RAY DIFFRACTION93
3.03-3.140.28421390.26035728X-RAY DIFFRACTION93
3.14-3.270.33881380.25665894X-RAY DIFFRACTION96
3.27-3.410.2841380.23835878X-RAY DIFFRACTION96
3.41-3.590.25841400.22025948X-RAY DIFFRACTION97
3.59-3.820.27071420.21546041X-RAY DIFFRACTION98
3.82-4.110.26451400.21486008X-RAY DIFFRACTION98
4.11-4.530.24291430.20026082X-RAY DIFFRACTION98
4.53-5.180.24561440.20326127X-RAY DIFFRACTION99
5.18-6.530.28981450.23786161X-RAY DIFFRACTION99

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