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- PDB-9iqn: CatM-W86A-L6R, a SnoaL-like protein in complex with substrate mim... -

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Basic information

Entry
Database: PDB / ID: 9iqn
TitleCatM-W86A-L6R, a SnoaL-like protein in complex with substrate mimic L6R
ComponentsSnoaL-like domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / CatM / SnoaL-like protein / complex / L6R
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: 2 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)14,8282
Polymers14,4331
Non-polymers3951
Water68538
1
A: SnoaL-like domain-containing protein
hetero molecules

A: SnoaL-like domain-containing protein
hetero molecules

A: SnoaL-like domain-containing protein
hetero molecules

A: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3118
Polymers57,7334
Non-polymers1,5784
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area9380 Å2
ΔGint-22 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.485, 68.485, 126.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

21A-326-

HOH

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Components

#1: Protein SnoaL-like domain-containing protein


Mass: 14433.339 Da / Num. of mol.: 1 / Mutation: W86A
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-A1D91 / (5~{R},6~{R})-6-[(~{E})-5-[(2~{S},3~{S},5~{R})-5-(2-hydroxyethyl)-3,5-dimethyl-oxolan-2-yl]-3-methyl-2-oxidanylidene-pent-3-enyl]-5-propyl-oxane-2,4-dione


Mass: 394.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H34O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM tri-Sodium citrate; pH 5.0 3.15 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→30.14 Å / Num. obs: 10579 / % possible obs: 93.53 % / Redundancy: 8.3 % / Biso Wilson estimate: 27.12 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.53
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 2.66 / Num. unique obs: 901 / CC1/2: 0.586

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Processing

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

9iq5


Resolution: 2→30.14 Å / SU ML: 0.2371 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 26.0194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2601 998 10.04 %
Rwork0.2257 8942 -
obs0.2292 9940 93.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.16 Å2
Refinement stepCycle: LAST / Resolution: 2→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 28 38 980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111954
X-RAY DIFFRACTIONf_angle_d1.07581284
X-RAY DIFFRACTIONf_chiral_restr0.0553147
X-RAY DIFFRACTIONf_plane_restr0.013166
X-RAY DIFFRACTIONf_dihedral_angle_d11.4277133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10.3321350.2711151X-RAY DIFFRACTION86.42
2.1-2.240.28361280.25391181X-RAY DIFFRACTION88.33
2.24-2.410.32681320.25551214X-RAY DIFFRACTION90.27
2.41-2.650.29161430.25231263X-RAY DIFFRACTION94.17
2.65-3.030.27861470.24281326X-RAY DIFFRACTION97.55
3.03-3.820.2641520.20611360X-RAY DIFFRACTION98.25
3.82-30.140.2141610.20621447X-RAY DIFFRACTION98.53
Refinement TLS params.Method: refined / Origin x: -27.4104011494 Å / Origin y: 15.9705929821 Å / Origin z: -16.5346257776 Å
111213212223313233
T0.234907552012 Å20.0550753512071 Å20.0735404924122 Å2-0.181256091646 Å2-0.056165874349 Å2--0.175454149431 Å2
L4.78616392643 °21.00435749944 °2-0.587937299304 °2-6.87750760951 °2-3.44911037041 °2--3.46090889448 °2
S-0.106535066798 Å °0.0592948022184 Å °-0.52516795464 Å °-0.259823911724 Å °-0.216564914295 Å °-0.419832597184 Å °0.217027266421 Å °0.318515153749 Å °0.153722326262 Å °
Refinement TLS groupSelection details: all

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