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- PDB-9m0a: Structure of TqaM from Penicillium aethiopicum in complex with D-... -

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Basic information

Entry
Database: PDB / ID: 9m0a
TitleStructure of TqaM from Penicillium aethiopicum in complex with D-(+)-3-phenyllactic acid
ComponentsTqaM
KeywordsMETAL BINDING PROTEIN / oxidative decarboxylation / biosynthesis / alpha-tertiary amino acids
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
(2R)-2-hydroxy-3-phenylpropanoic acid / : / TqaM
Similarity search - Component
Biological speciesPenicillium aethiopicum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsWang, H. / Mori, T. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of TqaM from Penicillium aethiopicum in complex with substrate
Authors: Wang, H. / Mori, T. / Abe, I.
History
DepositionFeb 24, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: TqaM
A: TqaM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,02610
Polymers68,3852
Non-polymers6418
Water8,809489
1
B: TqaM
A: TqaM
hetero molecules

B: TqaM
A: TqaM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,05220
Polymers136,7714
Non-polymers1,28116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area17530 Å2
ΔGint-177 kcal/mol
Surface area35960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.023, 139.258, 100.581
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

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Protein , 1 types, 2 molecules BA

#1: Protein TqaM


Mass: 34192.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium aethiopicum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: F1CWD8

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Non-polymers , 5 types, 497 molecules

#2: Chemical ChemComp-HF2 / (2R)-2-hydroxy-3-phenylpropanoic acid


Type: peptide-like / Mass: 166.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS (pH 5.5), 1 M ammonium sulfate, 1 % (w/v) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.81→46.51 Å / Num. obs: 59718 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 24.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 18.7
Reflection shellResolution: 1.81→1.85 Å / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3509 / CC1/2: 0.817

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.81→46.51 Å / SU ML: 0.1899 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 19.4221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.194 1908 3.34 %
Rwork0.162 55135 -
obs0.1631 57043 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.19 Å2
Refinement stepCycle: LAST / Resolution: 1.81→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4199 0 35 491 4725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00564333
X-RAY DIFFRACTIONf_angle_d0.75875888
X-RAY DIFFRACTIONf_chiral_restr0.0526654
X-RAY DIFFRACTIONf_plane_restr0.007770
X-RAY DIFFRACTIONf_dihedral_angle_d12.73331507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.860.27581210.22943467X-RAY DIFFRACTION84.8
1.86-1.910.23421230.22163596X-RAY DIFFRACTION88.04
1.91-1.960.23021270.21373673X-RAY DIFFRACTION90.69
1.96-2.020.23371300.18973794X-RAY DIFFRACTION93.05
2.02-2.10.20851340.17873901X-RAY DIFFRACTION95.03
2.1-2.180.22731380.17273918X-RAY DIFFRACTION95.95
2.18-2.280.22071330.17083956X-RAY DIFFRACTION96.69
2.28-2.40.20611410.17194007X-RAY DIFFRACTION97.58
2.4-2.550.23441400.17264031X-RAY DIFFRACTION98.23
2.55-2.750.20441400.16974073X-RAY DIFFRACTION98.92
2.75-3.020.21420.16014103X-RAY DIFFRACTION99.23
3.02-3.460.1721440.16144130X-RAY DIFFRACTION99.46
3.46-4.360.16731450.13414176X-RAY DIFFRACTION99.75
4.36-46.510.16791500.14824310X-RAY DIFFRACTION99.69

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