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- PDB-9n45: Crystal structure of none-heme iron enzyme (TqaM) from Trichoderm... -

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Basic information

Entry
Database: PDB / ID: 9n45
TitleCrystal structure of none-heme iron enzyme (TqaM) from Trichoderma atroviride bound with iron and 2-aminoisobutyric acid
ComponentsClass II aldolase/adducin N-terminal domain-containing protein
KeywordsMETAL BINDING PROTEIN / Oxidative decarboxylase
Function / homology
Function and homology information


actin filament binding / cytoskeleton
Similarity search - Function
: / 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
Similarity search - Domain/homology
ALPHA-AMINOISOBUTYRIC ACID / : / Class II aldolase/adducin N-terminal domain-containing protein
Similarity search - Component
Biological speciesTrichoderma atroviride (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLiu, S. / Zheng, Y.-C. / Chang, W.-C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of none-heme iron enzyme (TqaM) from Trichoderma atroviride bound with iron and 2-aminoisobutyric acid
Authors: Liu, S. / Zheng, Y.-C. / Chang, W.-C.
History
DepositionFeb 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)125,0668
Polymers124,7954
Non-polymers2714
Water10,773598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15170 Å2
ΔGint-129 kcal/mol
Surface area40610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.068, 124.174, 185.732
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
Components on special symmetry positions
IDModelComponents
11A-441-

HOH

21C-540-

HOH

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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.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AIB / ALPHA-AMINOISOBUTYRIC ACID


Type: L-peptide linking / Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.64 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Calcium acetate, 0.1 M Sodium cacodylate, pH 5.5, 12% (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: Jul 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→17.44 Å / Num. obs: 71125 / % possible obs: 99.2 % / Redundancy: 12.1 % / Biso Wilson estimate: 27.4 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.159 / Χ2: 1.02 / Net I/σ(I): 10.8
Reflection shellResolution: 2.15→2.2 Å / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4543 / CC1/2: 0.831 / Χ2: 0.65

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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: 2.15→17.44 Å / SU ML: 0.2733 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1132
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25 3523 4.96 %
Rwork0.2168 67563 -
obs0.2185 71086 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.07 Å2
Refinement stepCycle: LAST / Resolution: 2.15→17.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8738 0 10 598 9346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00368971
X-RAY DIFFRACTIONf_angle_d0.574112163
X-RAY DIFFRACTIONf_chiral_restr0.04451324
X-RAY DIFFRACTIONf_plane_restr0.00451600
X-RAY DIFFRACTIONf_dihedral_angle_d14.753299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.29181550.2612660X-RAY DIFFRACTION100
2.18-2.210.34591420.25352702X-RAY DIFFRACTION100
2.21-2.240.26571330.24542702X-RAY DIFFRACTION100
2.24-2.280.27041310.26262730X-RAY DIFFRACTION100
2.28-2.320.31951340.24812670X-RAY DIFFRACTION99.96
2.32-2.360.26271630.24772670X-RAY DIFFRACTION100
2.36-2.40.29471340.26182721X-RAY DIFFRACTION100
2.4-2.440.32031270.25452678X-RAY DIFFRACTION100
2.44-2.490.30741540.25052728X-RAY DIFFRACTION100
2.49-2.550.2821290.24512701X-RAY DIFFRACTION100
2.55-2.610.31241420.24652701X-RAY DIFFRACTION100
2.61-2.670.28221420.24512692X-RAY DIFFRACTION100
2.67-2.740.28091390.2412720X-RAY DIFFRACTION99.97
2.74-2.820.26261580.22892712X-RAY DIFFRACTION100
2.82-2.920.28441590.23552705X-RAY DIFFRACTION99.97
2.92-3.020.3091320.23772720X-RAY DIFFRACTION100
3.02-3.140.2481340.23292720X-RAY DIFFRACTION99.96
3.14-3.280.26771290.22022719X-RAY DIFFRACTION99.82
3.28-3.450.2761420.21972727X-RAY DIFFRACTION99.69
3.45-3.670.2251650.2122702X-RAY DIFFRACTION99.2
3.67-3.950.21671450.1932660X-RAY DIFFRACTION98.32
3.95-4.340.22291160.18492691X-RAY DIFFRACTION96.79
4.34-4.950.18661290.17222696X-RAY DIFFRACTION96.68
4.95-6.190.21051240.18692705X-RAY DIFFRACTION96.62
6.2-17.440.16721650.16862731X-RAY DIFFRACTION95.7

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