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- PDB-8w0n: IRED crystal structure -

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Basic information

Entry
Database: PDB / ID: 8w0n
TitleIRED crystal structure
ComponentsIRED
KeywordsOXIDOREDUCTASE / protein engineering / imine reductase / scalable manufacturing
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsPeat, T.S. / Newman, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2024
Title: Enhancing the Imine Reductase Activity of a Promiscuous Glucose Dehydrogenase for Scalable Manufacturing of a Chiral Neprilysin Inhibitor Precursor
Authors: Yi, X. / Kleinbeck, F. / Ching, C. / Boghospor, L. / Gomes, S. / Alvizo, O. / Allmendinger, T. / Fell, J. / Subramanian, N. / Li, M. / Garcia, R. / Riggins, J. / Entwistle, D. / Richter, Y. ...Authors: Yi, X. / Kleinbeck, F. / Ching, C. / Boghospor, L. / Gomes, S. / Alvizo, O. / Allmendinger, T. / Fell, J. / Subramanian, N. / Li, M. / Garcia, R. / Riggins, J. / Entwistle, D. / Richter, Y. / Gschwend, D. / Lauener, L. / Peat, T.S. / Lebhar, H. / Schlama, T. / Ruch, T.
History
DepositionFeb 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 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: IRED
B: IRED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7447
Polymers56,1382
Non-polymers1,6065
Water8,323462
1
A: IRED
B: IRED
hetero molecules

A: IRED
B: IRED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,48814
Polymers112,2764
Non-polymers3,21210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area19390 Å2
ΔGint-145 kcal/mol
Surface area33830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.844, 127.698, 63.598
Angle α, β, γ (deg.)90.000, 109.381, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-567-

HOH

21A-607-

HOH

31B-610-

HOH

41B-629-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 258 / Label seq-ID: 1 - 258

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein IRED


Mass: 28068.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 467 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: Crystals were found in 20% PEG3350 with 200 mM sodium dihydrogen phosphate when set up in sitting drop plates with 200 nL reservoir and 200 nL of 12 mg/mL protein in SD-2 plates at room temperature.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.37→48.5 Å / Num. obs: 102543 / % possible obs: 99.6 % / Redundancy: 20.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.023 / Net I/σ(I): 17.6
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 18 % / Rmerge(I) obs: 0.985 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 4726 / CC1/2: 0.914 / Rpim(I) all: 0.233 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→48.5 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.327 / SU ML: 0.025 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.044
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1438 5158 5.032 %
Rwork0.1188 97349 -
all0.12 --
obs-102507 99.597 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.548 Å2
Baniso -1Baniso -2Baniso -3
1-0.688 Å20 Å2-0.523 Å2
2--0.899 Å20 Å2
3----0.977 Å2
Refinement stepCycle: LAST / Resolution: 1.37→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3894 0 104 462 4460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124303
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164104
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.6425878
X-RAY DIFFRACTIONr_angle_other_deg0.5751.5689509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8735558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.663513
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.02352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49110732
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.79210164
X-RAY DIFFRACTIONr_chiral_restr0.10.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02888
X-RAY DIFFRACTIONr_nbd_refined0.230.2922
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.23746
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22180
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2309
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1910.244
X-RAY DIFFRACTIONr_nbd_other0.2130.2158
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1830.287
X-RAY DIFFRACTIONr_mcbond_it1.2381.5752175
X-RAY DIFFRACTIONr_mcbond_other1.2291.5752175
X-RAY DIFFRACTIONr_mcangle_it1.5522.8352752
X-RAY DIFFRACTIONr_mcangle_other1.5522.8362753
X-RAY DIFFRACTIONr_scbond_it1.7451.8742128
X-RAY DIFFRACTIONr_scbond_other1.7451.8732125
X-RAY DIFFRACTIONr_scangle_it2.3263.3173126
X-RAY DIFFRACTIONr_scangle_other2.3273.3143121
X-RAY DIFFRACTIONr_lrange_it2.96620.82319656
X-RAY DIFFRACTIONr_lrange_other2.95320.7519639
X-RAY DIFFRACTIONr_rigid_bond_restr4.25638407
X-RAY DIFFRACTIONr_ncsr_local_group_10.060.058931
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.059960.0501
12AX-RAY DIFFRACTIONLocal ncs0.059960.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.4010.2133590.1836910X-RAY DIFFRACTION95.032
1.401-1.440.1653800.1286968X-RAY DIFFRACTION99.8912
1.44-1.4820.1583460.1076848X-RAY DIFFRACTION99.9444
1.482-1.5270.1283370.0936644X-RAY DIFFRACTION99.8427
1.527-1.5770.1283130.0846457X-RAY DIFFRACTION99.9409
1.577-1.6320.1153370.086242X-RAY DIFFRACTION99.9848
1.632-1.6940.1183120.0755991X-RAY DIFFRACTION99.9841
1.694-1.7630.1162970.0795810X-RAY DIFFRACTION99.9836
1.763-1.8410.1292950.0865533X-RAY DIFFRACTION99.9828
1.841-1.9310.1392690.15321X-RAY DIFFRACTION99.9821
1.931-2.0350.1422630.1165045X-RAY DIFFRACTION100
2.035-2.1590.1452700.1224756X-RAY DIFFRACTION100
2.159-2.3070.1412580.1114476X-RAY DIFFRACTION100
2.307-2.4920.1372180.114180X-RAY DIFFRACTION100
2.492-2.7290.1452250.1183826X-RAY DIFFRACTION100
2.729-3.050.1721880.1363482X-RAY DIFFRACTION100
3.05-3.5190.1461590.1413097X-RAY DIFFRACTION100
3.519-4.3040.1241560.1252594X-RAY DIFFRACTION100
4.304-6.0630.1721100.1492023X-RAY DIFFRACTION100
6.063-48.50.16660.1681146X-RAY DIFFRACTION100

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