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- PDB-9iqk: SacM in complex with LC3 -

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Basic information

Entry
Database: PDB / ID: 9iqk
TitleSacM in complex with LC3
ComponentsNuclear transport factor 2 family protein
KeywordsBIOSYNTHETIC PROTEIN / Compelex / SacM / SnoaL-like protein / polyketide LC3
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / : / Nuclear transport factor 2 family protein
Function and homology information
Biological speciesSaccharothrix syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, B. / Ge, H.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22277051,81925033, 22193071 China
CitationJournal: To Be Published
Title: Tandem Michael addition and Knoevenagel condensation catalyzed by NTF2-Like Enzymes as iminium catalysis
Authors: Liu, C.L. / Zhang, B. / Ge, H.M.
History
DepositionJul 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear transport factor 2 family protein
B: Nuclear transport factor 2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6034
Polymers29,8142
Non-polymers7892
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-14 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.250, 52.250, 202.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Nuclear transport factor 2 family protein


Mass: 14906.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix syringae (bacteria) / Strain: NRRL B-16468 / Gene: EKG83_24495
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A5Q0H2K6
#2: Chemical ChemComp-A1D9Z / (2~{R},3~{R})-4-oxidanyl-3-propyl-2-[(3~{E},6~{S},7~{S},9~{E})-3,7,9-trimethyl-6,11-bis(oxidanyl)-2-oxidanylidene-undeca-3,9-dienyl]-2,3-dihydropyran-6-one


Mass: 394.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H34O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M Ammonium sulfate, 0.1 M Sodium HEPES 7.5, 2 % v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97851 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 1.8→34.71 Å / Num. obs: 26342 / % possible obs: 96.98 % / Redundancy: 9.5 % / Biso Wilson estimate: 22.16 Å2 / CC1/2: 0.995 / Net I/σ(I): 11.34
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 2525 / CC1/2: 0.889

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9IQ7

9iq7


Resolution: 1.8→34.71 Å / SU ML: 0.1709 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7683
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2318 1999 7.59 %
Rwork0.1961 24338 -
obs0.1987 26337 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.25 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 56 154 2123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622039
X-RAY DIFFRACTIONf_angle_d0.91332761
X-RAY DIFFRACTIONf_chiral_restr0.0589306
X-RAY DIFFRACTIONf_plane_restr0.0081362
X-RAY DIFFRACTIONf_dihedral_angle_d11.194303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.27681370.21891679X-RAY DIFFRACTION96.91
1.85-1.890.25651360.1941656X-RAY DIFFRACTION95.07
1.89-1.950.2331380.20761675X-RAY DIFFRACTION95.17
1.95-2.010.24751370.19041681X-RAY DIFFRACTION95.38
2.01-2.090.21251390.1791679X-RAY DIFFRACTION96.14
2.09-2.170.24131390.17861689X-RAY DIFFRACTION95.76
2.17-2.270.22591380.19491690X-RAY DIFFRACTION95.56
2.27-2.390.25121390.1911693X-RAY DIFFRACTION95.32
2.39-2.540.23591420.20651719X-RAY DIFFRACTION96.98
2.54-2.730.27481430.21131738X-RAY DIFFRACTION97.31
2.73-3.010.23111450.20581777X-RAY DIFFRACTION98.92
3.01-3.440.23461500.20341817X-RAY DIFFRACTION99.49
3.44-4.340.19751520.18191860X-RAY DIFFRACTION99.8
4.34-34.710.23471640.19791985X-RAY DIFFRACTION99.95
Refinement TLS params.Method: refined / Origin x: 13.6529452779 Å / Origin y: -11.2139791579 Å / Origin z: -15.2446842494 Å
111213212223313233
T0.113445291646 Å20.00507011400598 Å20.00799276209878 Å2-0.189037423302 Å2-0.00131753873419 Å2--0.109298055277 Å2
L2.79677222946 °2-0.0654133964583 °2-0.18925170927 °2-1.49790233132 °20.462400469093 °2--1.33519887927 °2
S0.0139202432754 Å °0.163584530147 Å °-0.137005842537 Å °-0.0351811999867 Å °-0.0130541330194 Å °-0.0655893168635 Å °0.0279079828643 Å °0.166889500719 Å °0.0332818910382 Å °
Refinement TLS groupSelection details: all

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