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- PDB-9iql: SacM in complex with L6S -

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Basic information

Entry
Database: PDB / ID: 9iql
TitleSacM in complex with L6S
ComponentsNuclear transport factor 2 family protein
KeywordsBIOSYNTHETIC PROTEIN / SacM / SnoaL-like protein / Complex / macrocyclase
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / : / DI(HYDROXYETHYL)ETHER / Nuclear transport factor 2 family protein
Function and homology information
Biological speciesSaccharothrix syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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)30,9298
Polymers29,8142
Non-polymers1,1156
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-22 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.239, 52.239, 203.458
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
Components on special symmetry positions
IDModelComponents
11A-360-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 141 molecules

#2: Chemical ChemComp-A1D90 / (5~{R},6~{R})-6-[(~{E})-5-[(2~{S},3~{S},5~{S})-5-(2-hydroxyethyl)-3,5-dimethyl-oxolan-2-yl]-3-methyl-2-oxidanylidene-pent-3-enyl]-5-propyl-oxane-2,4-dione / 6-O-sulfo-alpha-L-galactose / 6-O-sulfo-L-galactose / 6-O-sulfo-galactose


Mass: 394.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H34O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density % sol: 47.16 %
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: BL10U2 / Wavelength: 0.97853 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.65→36.34 Å / Num. obs: 32718 / % possible obs: 92.65 % / Redundancy: 15.1 % / Biso Wilson estimate: 21.39 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.62
Reflection shellResolution: 1.65→1.71 Å / Num. unique obs: 3433 / CC1/2: 0.846

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Processing

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

9iq7


Resolution: 1.65→36.34 Å / SU ML: 0.161 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2248 1606 4.92 %
Rwork0.2095 31059 -
obs0.2102 32665 92.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.8 Å2
Refinement stepCycle: LAST / Resolution: 1.65→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 76 135 2126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00932066
X-RAY DIFFRACTIONf_angle_d1.06182799
X-RAY DIFFRACTIONf_chiral_restr0.0677311
X-RAY DIFFRACTIONf_plane_restr0.0105362
X-RAY DIFFRACTIONf_dihedral_angle_d12.8377291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.31390.25112971X-RAY DIFFRACTION99.9
1.7-1.760.25551480.22513002X-RAY DIFFRACTION99.94
1.76-1.830.24461450.20852971X-RAY DIFFRACTION100
1.83-1.90.2531330.22142178X-RAY DIFFRACTION85.06
1.93-2.020.24521060.21942322X-RAY DIFFRACTION86.56
2.02-2.140.21031270.20082742X-RAY DIFFRACTION91.22
2.14-2.310.26371550.25032715X-RAY DIFFRACTION89.97
2.31-2.540.23731390.22233068X-RAY DIFFRACTION99.97
2.54-2.910.25751630.22432863X-RAY DIFFRACTION93.68
2.91-3.640.22331800.20463028X-RAY DIFFRACTION100
3.68-36.340.1891710.18813199X-RAY DIFFRACTION97.57
Refinement TLS params.Method: refined / Origin x: 13.6749211931 Å / Origin y: -11.3452442082 Å / Origin z: -15.2530594383 Å
111213212223313233
T0.113854989061 Å20.0123120410158 Å20.00691673816256 Å2-0.203226380491 Å2-0.00468513179247 Å2--0.120195159787 Å2
L3.42886785278 °20.0261055507263 °20.472549564197 °2-1.7361629673 °20.414415447522 °2--1.70745671822 °2
S0.0363994977498 Å °0.207127641682 Å °-0.111284692195 Å °-0.0108083250916 Å °-0.0346834809166 Å °-0.0577184776369 Å °0.0429159384998 Å °0.226789077596 Å °0.0405714259414 Å °
Refinement TLS groupSelection details: all

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