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- PDB-9iqd: Apo-MicM,homologous of AkaM, SnoaL-like protein -

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Basic information

Entry
Database: PDB / ID: 9iqd
TitleApo-MicM,homologous of AkaM, SnoaL-like protein
ComponentsSnoaL-like domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / MicM / homologous of AkaM / SnoaL-like protein / Apo form
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / CITRIC ACID / DI(HYDROXYETHYL)ETHER / SnoaL-like domain-containing protein
Function and homology information
Biological speciesMicromonospora sp. HM134 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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: SnoaL-like domain-containing protein
B: SnoaL-like domain-containing protein
C: SnoaL-like domain-containing protein
D: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,15120
Polymers57,9734
Non-polymers1,17716
Water9,044502
1
A: SnoaL-like domain-containing protein
hetero molecules

D: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4269
Polymers28,9872
Non-polymers4397
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2280 Å2
ΔGint-14 kcal/mol
Surface area12210 Å2
MethodPISA
2
B: SnoaL-like domain-containing protein
C: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,72411
Polymers28,9872
Non-polymers7389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-13 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.306, 72.732, 65.403
Angle α, β, γ (deg.)90.000, 112.210, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
SnoaL-like domain-containing protein


Mass: 14493.354 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora sp. HM134 (bacteria) / Gene: FJK98_13695
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A518WFQ2

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Non-polymers , 5 types, 518 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20 % w/v Polyethylene glycol 6,000, 100 mM tri-Sodium citrate; pH 5.0

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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: 1.77→59.54 Å / Num. obs: 53998 / % possible obs: 99.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 23.98 Å2 / CC1/2: 0.997 / Net I/σ(I): 14.13
Reflection shellResolution: 1.77→1.83 Å / Num. unique obs: 5331 / CC1/2: 0.937

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Processing

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

9iq7


Resolution: 1.77→59.54 Å / SU ML: 0.1909 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.835
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2165 2766 5.13 %
Rwork0.1815 51196 -
obs0.1832 53962 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.75 Å2
Refinement stepCycle: LAST / Resolution: 1.77→59.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3655 0 76 503 4234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663787
X-RAY DIFFRACTIONf_angle_d0.88645094
X-RAY DIFFRACTIONf_chiral_restr0.0577554
X-RAY DIFFRACTIONf_plane_restr0.0094676
X-RAY DIFFRACTIONf_dihedral_angle_d7.8408541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.80.22861270.23072535X-RAY DIFFRACTION98.7
1.8-1.830.27541330.21842534X-RAY DIFFRACTION98.63
1.83-1.870.23641370.21042558X-RAY DIFFRACTION98.83
1.87-1.910.27981320.20062525X-RAY DIFFRACTION98.63
1.91-1.950.23081380.2012562X-RAY DIFFRACTION99.08
1.95-1.990.22171380.19262541X-RAY DIFFRACTION99.11
1.99-2.040.23031420.18332538X-RAY DIFFRACTION99.04
2.04-2.10.23891390.18592546X-RAY DIFFRACTION99.3
2.1-2.160.23121480.18352550X-RAY DIFFRACTION99.26
2.16-2.230.19491390.1822543X-RAY DIFFRACTION99.41
2.23-2.310.22771440.18822568X-RAY DIFFRACTION99.45
2.31-2.40.23861390.19352570X-RAY DIFFRACTION99.56
2.4-2.510.23871450.18622566X-RAY DIFFRACTION99.49
2.51-2.640.23781390.19622575X-RAY DIFFRACTION99.78
2.64-2.810.20351370.19032572X-RAY DIFFRACTION99.6
2.81-3.030.19681560.18822559X-RAY DIFFRACTION99.45
3.03-3.330.24651340.18352579X-RAY DIFFRACTION99.27
3.33-3.810.19991260.16352587X-RAY DIFFRACTION98.91
3.81-4.80.17021320.1492581X-RAY DIFFRACTION98.83
4.8-59.540.22961410.18842607X-RAY DIFFRACTION97.9
Refinement TLS params.Method: refined / Origin x: 29.6025894931 Å / Origin y: -1.17660088713 Å / Origin z: 31.9495865714 Å
111213212223313233
T0.217267872181 Å20.00989874901206 Å2-0.0024832082843 Å2-0.175504677565 Å2-0.0104157177641 Å2--0.203126268319 Å2
L1.08384901116 °2-0.0220234036257 °20.0433139324974 °2-0.129283341649 °2-0.0382442255487 °2--0.0657428672566 °2
S-0.0378123528906 Å °-0.0229620824228 Å °-0.0335604771975 Å °0.0114449499666 Å °0.041933383283 Å °-0.0216289981194 Å °0.012388673139 Å °0.0138099225769 Å °-0.00251312964205 Å °
Refinement TLS groupSelection details: all

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