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- PDB-8jyt: Ancestral imine reducatase N560 -

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Basic information

Entry
Database: PDB / ID: 8jyt
TitleAncestral imine reducatase N560
Componentsancestra imine reductase
KeywordsDE NOVO PROTEIN / ancestral sequence reconstruction / imine reductase
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsZhu, X.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21878085 China
CitationJournal: To Be Published
Title: The structure of ancestral imine reductase N560.
Authors: Zhu, X.X. / Zheng, G.W.
History
DepositionJul 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ancestra imine reductase
B: ancestra imine reductase
C: ancestra imine reductase
D: ancestra imine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5548
Polymers125,5814
Non-polymers2,9744
Water6,143341
1
A: ancestra imine reductase
C: ancestra imine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2774
Polymers62,7902
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-84 kcal/mol
Surface area20760 Å2
MethodPISA
2
B: ancestra imine reductase
hetero molecules

D: ancestra imine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2774
Polymers62,7902
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area10220 Å2
ΔGint-80 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.900, 68.570, 84.240
Angle α, β, γ (deg.)76.25, 67.75, 60.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
ancestra imine reductase


Mass: 31395.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: Calcium chloride dihydrate, sodium acetate, MPD

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Data collection

DiffractionMean temperature: 77.36 K / Ambient temp details: -196 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.79→32.99 Å / Num. obs: 110068 / % possible obs: 96.6 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.02 / Rrim(I) all: 0.038 / Χ2: 0.93 / Net I/σ(I): 15.8 / Num. measured all: 387555
Reflection shellResolution: 1.79→1.84 Å / % possible obs: 95.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.625 / Num. measured all: 25409 / Num. unique obs: 7994 / CC1/2: 0.823 / Rpim(I) all: 0.42 / Rrim(I) all: 0.758 / Χ2: 0.86 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDS0.7.7 : 23/04/21data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→27.79 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 32.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 2017 1.83 %
Rwork0.2064 --
obs0.2066 109969 96.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8399 0 192 341 8932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d10.2131313
X-RAY DIFFRACTIONf_chiral_restr0.0461374
X-RAY DIFFRACTIONf_plane_restr0.0171577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.40181510.38977572X-RAY DIFFRACTION95
1.83-1.880.44151430.35947647X-RAY DIFFRACTION96
1.88-1.940.36321450.31937623X-RAY DIFFRACTION96
1.94-20.3321350.29227721X-RAY DIFFRACTION96
2-2.070.29731430.26827701X-RAY DIFFRACTION96
2.07-2.160.25581400.24517750X-RAY DIFFRACTION97
2.16-2.260.25871510.23667666X-RAY DIFFRACTION97
2.26-2.370.281540.23047765X-RAY DIFFRACTION97
2.37-2.520.24751420.2267691X-RAY DIFFRACTION97
2.52-2.720.2591430.22537763X-RAY DIFFRACTION97
2.72-2.990.2521390.22337781X-RAY DIFFRACTION97
2.99-3.420.23261480.20917784X-RAY DIFFRACTION98
3.42-4.310.18651390.17627823X-RAY DIFFRACTION98
4.31-27.790.15651440.16117665X-RAY DIFFRACTION96

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