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- PDB-9iq3: AkaM,SnoaL-lile Protein -

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Basic information

Entry
Database: PDB / ID: 9iq3
TitleAkaM,SnoaL-lile Protein
ComponentsAkaM
KeywordsBIOSYNTHETIC PROTEIN / SnoaL-Like protein catalyze tandem cyclizations
Biological speciesStreptomyces sp. NPS-554 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, B. / Ma, X.X. / Zhu, A. / 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: AkaM
B: AkaM
C: AkaM
D: AkaM


Theoretical massNumber of molelcules
Total (without water)58,0134
Polymers58,0134
Non-polymers00
Water724
1
A: AkaM
D: AkaM


Theoretical massNumber of molelcules
Total (without water)29,0072
Polymers29,0072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-9 kcal/mol
Surface area11560 Å2
MethodPISA
2
B: AkaM
C: AkaM


Theoretical massNumber of molelcules
Total (without water)29,0072
Polymers29,0072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-9 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.167, 74.167, 108.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
AkaM


Mass: 14503.253 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: WP_062216200.1 / Source: (gene. exp.) Streptomyces sp. NPS-554 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium citrate tribasic dihydrate; 0.1 M Sodium HEPES 7.5; 20 % v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→52.44 Å / Num. obs: 20398 / % possible obs: 99.53 % / Redundancy: 2 % / CC1/2: 0.994 / Net I/σ(I): 6.34
Reflection shellResolution: 2.5→2.565 Å / Num. unique obs: 19471 / CC1/2: 0.715

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→37.08 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 930 4.57 %RANDOM
Rwork0.1973 ---
obs0.1981 20362 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3632 0 0 4 3636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063700
X-RAY DIFFRACTIONf_angle_d1.3064988
X-RAY DIFFRACTIONf_dihedral_angle_d16.4821348
X-RAY DIFFRACTIONf_chiral_restr0.086534
X-RAY DIFFRACTIONf_plane_restr0.005662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.14591460.1182742X-RAY DIFFRACTION100
2.63-2.80.16251710.13362732X-RAY DIFFRACTION100
2.8-3.010.18181160.17682783X-RAY DIFFRACTION100
3.01-3.320.19751070.17992792X-RAY DIFFRACTION100
3.32-3.790.18411280.20522773X-RAY DIFFRACTION100
3.79-4.780.27881190.20872813X-RAY DIFFRACTION99
4.79-37.080.23491430.22532797X-RAY DIFFRACTION99

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