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- PDB-9iqm: CatM-L6S, a SnoaL-like protein in complex with substrate mimic L6S -

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Basic information

Entry
Database: PDB / ID: 9iqm
TitleCatM-L6S, a SnoaL-like protein in complex with substrate mimic L6S
ComponentsSnoaL-like domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / CatM / complex / L6S
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / : / SnoaL-like domain-containing protein
Function and homology information
Biological speciesStreptantibioticus cattleyicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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Assembly

Deposited unit
A: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0393
Polymers14,5481
Non-polymers4912
Water1,15364
1
A: SnoaL-like domain-containing protein
hetero molecules

A: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0786
Polymers29,0972
Non-polymers9814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2730 Å2
ΔGint-40 kcal/mol
Surface area12280 Å2
MethodPISA
2
A: SnoaL-like domain-containing protein
hetero molecules

A: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0786
Polymers29,0972
Non-polymers9814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2120 Å2
ΔGint-41 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.617, 99.719, 58.859
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein SnoaL-like domain-containing protein


Mass: 14548.470 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptantibioticus cattleyicolor (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057) (bacteria)
Gene: SCATT_01420
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G8X1I4
#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.: 1 / Source method: obtained synthetically / Formula: C22H34O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 64 / 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: 1.95 Å3/Da / Density % sol: 36.84 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
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: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.7→36.01 Å / Num. obs: 12789 / % possible obs: 98.97 % / Redundancy: 10.2 % / Biso Wilson estimate: 20.86 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.37
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 2.38 / Num. unique obs: 1178 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9IQ5

9iq5


Resolution: 1.7→36.01 Å / SU ML: 0.1754 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4214
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229 651 5.1 %
Rwork0.2078 12126 -
obs0.2089 12777 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 0 33 64 1020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095969
X-RAY DIFFRACTIONf_angle_d1.14251306
X-RAY DIFFRACTIONf_chiral_restr0.0652147
X-RAY DIFFRACTIONf_plane_restr0.0086167
X-RAY DIFFRACTIONf_dihedral_angle_d14.1306133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.2551340.24292288X-RAY DIFFRACTION95.47
1.83-2.020.22271340.21732394X-RAY DIFFRACTION99.61
2.02-2.310.19831130.19572438X-RAY DIFFRACTION99.88
2.31-2.910.23671450.23372434X-RAY DIFFRACTION99.92
2.91-36.010.23111250.19462572X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: -5.52419127717 Å / Origin y: -13.9472791272 Å / Origin z: 4.01525036268 Å
111213212223313233
T0.14734911134 Å20.00582876704449 Å2-0.0191944586886 Å2-0.133056041293 Å20.0113890570164 Å2--0.13794504614 Å2
L2.35291719568 °2-0.0394518397716 °20.819887257978 °2-0.939911433777 °20.275021819817 °2--1.88216359164 °2
S-0.164645528681 Å °0.166316722535 Å °0.205575921964 Å °-0.154486064229 Å °-0.0253049860647 Å °0.0711434068938 Å °-0.0533408785662 Å °-0.0118343809679 Å °0.148106905537 Å °
Refinement TLS groupSelection details: all

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