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- PDB-9iq7: SacM-homologous of AkaM -

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Basic information

Entry
Database: PDB / ID: 9iq7
TitleSacM-homologous of AkaM
ComponentsNuclear transport factor 2 family protein
KeywordsBIOSYNTHETIC PROTEIN / SnoaL-like protein / Macrocyclase / Apo-form
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / Nuclear transport factor 2 family protein
Function and homology information
Biological speciesSaccharothrix syringae (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: Nuclear transport factor 2 family protein
B: Nuclear transport factor 2 family protein


Theoretical massNumber of molelcules
Total (without water)29,8142
Polymers29,8142
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-13 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.182, 52.182, 202.928
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-247-

HOH

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Components

#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) / Gene: EKG83_24495
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A5Q0H2K6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
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: 1.77→50.73 Å / Num. obs: 27227 / % possible obs: 95.5 % / Redundancy: 15.1 % / Biso Wilson estimate: 29.68 Å2 / CC1/2: 0.995 / Net I/σ(I): 26.03
Reflection shellResolution: 1.77→1.83 Å / Num. unique obs: 2760 / CC1/2: 0.901

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→50.73 Å / SU ML: 0.2114 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.0056
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2232 1417 5.2 %
Rwork0.2029 25810 -
obs0.204 27227 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.55 Å2
Refinement stepCycle: LAST / Resolution: 1.77→50.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 0 112 2057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651982
X-RAY DIFFRACTIONf_angle_d0.92932678
X-RAY DIFFRACTIONf_chiral_restr0.0584296
X-RAY DIFFRACTIONf_plane_restr0.0099349
X-RAY DIFFRACTIONf_dihedral_angle_d5.8178265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.830.30021440.23062617X-RAY DIFFRACTION99.96
1.83-1.910.23181430.19672640X-RAY DIFFRACTION99.96
1.91-1.990.21861140.20342294X-RAY DIFFRACTION86.06
1.99-2.10.25431130.19942378X-RAY DIFFRACTION88.87
2.1-2.230.19721420.19722658X-RAY DIFFRACTION100
2.23-2.40.24171290.21152469X-RAY DIFFRACTION92.16
2.4-2.640.27041390.23452718X-RAY DIFFRACTION100
2.64-3.030.23251490.21192584X-RAY DIFFRACTION96.06
3.03-3.810.22751730.19872574X-RAY DIFFRACTION94.08
3.81-50.730.21710.19242878X-RAY DIFFRACTION97.69
Refinement TLS params.Method: refined / Origin x: 12.4126813606 Å / Origin y: -14.6175411167 Å / Origin z: -15.1633549135 Å
111213212223313233
T0.169796321913 Å20.00603140397822 Å20.0078218220029 Å2-0.236427218696 Å20.00450025428959 Å2--0.155618895742 Å2
L2.5806769977 °20.103372561866 °20.302774210386 °2-1.79874675176 °2-0.50124189309 °2--1.49061482837 °2
S-0.0143565223056 Å °0.0238245929061 Å °0.0731673262498 Å °0.0178495425985 Å °0.0387096133229 Å °0.0892732329449 Å °-0.039795869363 Å °-0.159590358949 Å °-0.00466608118685 Å °
Refinement TLS groupSelection details: all

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