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- PDB-9n43: Crystal structure of none-heme iron enzyme (TqaM) from Trichoderm... -

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Basic information

Entry
Database: PDB / ID: 9n43
TitleCrystal structure of none-heme iron enzyme (TqaM) from Trichoderma atroviride bound with iron
ComponentsClass II aldolase/adducin N-terminal domain-containing protein
KeywordsMETAL BINDING PROTEIN / Oxidative decarboxylase
Function / homology: / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / actin filament binding / cytoskeleton / : / Class II aldolase/adducin N-terminal domain-containing protein
Function and homology information
Biological speciesTrichoderma atroviride (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLiu, S. / Zheng, Y.-C. / Chang, W.-C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Directed Evolution and Unusual Protonation Mechanism of Pyridoxal Radical C-C Coupling Enzymes for the Enantiodivergent Photobiocatalytic Synthesis of Noncanonical Amino Acids.
Authors: Cheng, L. / Bo, Z. / Krohn-Hansen, B. / Yang, Y.
History
DepositionFeb 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2026Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Class II aldolase/adducin N-terminal domain-containing protein
B: Class II aldolase/adducin N-terminal domain-containing protein
C: Class II aldolase/adducin N-terminal domain-containing protein
D: Class II aldolase/adducin N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,0188
Polymers124,7954
Non-polymers2234
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15120 Å2
ΔGint-142 kcal/mol
Surface area40920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.513, 124.972, 187.295
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
Class II aldolase/adducin N-terminal domain-containing protein


Mass: 31198.732 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma atroviride (fungus) / Gene: TRIATDRAFT_52267 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9NNG6
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Magnesium acetate, 0.1 M Sodium acetate pH 4.5, 8% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→18.25 Å / Num. obs: 40872 / % possible obs: 98.4 % / Redundancy: 5.3 % / CC1/2: 0.908 / Rmerge(I) obs: 0.234 / Net I/σ(I): 5.3
Reflection shellResolution: 2.6→2.71 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4617 / CC1/2: 0.568

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→18.25 Å / SU ML: 0.3879 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 27.7908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2917 2045 5.01 %
Rwork0.2604 38810 -
obs0.262 40855 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.6 Å2
Refinement stepCycle: LAST / Resolution: 2.6→18.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8706 0 4 250 8960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218953
X-RAY DIFFRACTIONf_angle_d0.486512142
X-RAY DIFFRACTIONf_chiral_restr0.04211322
X-RAY DIFFRACTIONf_plane_restr0.00411599
X-RAY DIFFRACTIONf_dihedral_angle_d14.36783296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.37351470.32152570X-RAY DIFFRACTION99.6
2.66-2.730.32421390.31582594X-RAY DIFFRACTION99.6
2.73-2.80.34381400.29132558X-RAY DIFFRACTION99.37
2.8-2.880.33291240.29072599X-RAY DIFFRACTION99.67
2.88-2.970.31221340.28872631X-RAY DIFFRACTION99.96
2.97-3.080.33351170.28782607X-RAY DIFFRACTION99.93
3.08-3.20.29641210.27162615X-RAY DIFFRACTION99.85
3.2-3.350.29191570.26392582X-RAY DIFFRACTION99.67
3.35-3.520.28351650.26822602X-RAY DIFFRACTION99.82
3.52-3.740.29521440.2472585X-RAY DIFFRACTION99.13
3.74-4.030.27421340.24092589X-RAY DIFFRACTION98.09
4.03-4.430.2511300.22932563X-RAY DIFFRACTION97.05
4.43-5.060.25711300.21572543X-RAY DIFFRACTION96.15
5.06-6.330.22881120.23232605X-RAY DIFFRACTION96.25
6.33-18.250.2231510.19492567X-RAY DIFFRACTION93.53

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