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- PDB-8tcc: GTP Cyclohydrolase-IB with dehydrocostus lactone -

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Basic information

Entry
Database: PDB / ID: 8tcc
TitleGTP Cyclohydrolase-IB with dehydrocostus lactone
ComponentsGTP cyclohydrolase FolE2
KeywordsHYDROLASE/INHIBITOR / Cyclohydrolase / GTP / dehydrocostus lactone / fole2 / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


: / GTP cyclohydrolase I / GTP cyclohydrolase I activity
Similarity search - Function
GTP cyclohydrolase FolE2/MptA / GTP cyclohydrolase FolE2 / Type I GTP cyclohydrolase folE2
Similarity search - Domain/homology
: / SULFITE ION / : / GTP cyclohydrolase FolE2
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMcWhorter, K.L. / Amaya Lopez, C.Y. / Davis, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM147557 United States
CitationJournal: To be published
Title: Combatting melioidosis with chemical synthetic lethality
Authors: Zhang, Y. / McWhorter, K.L. / Rosen, P. / Klaus, J. / Gallant, E. / Amaya Lopez, C.Y. / Jhunjhunwala, R. / Chandler, J. / Davis, K.M. / Seyedsayamdost, M.R.
History
DepositionJun 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP cyclohydrolase FolE2
B: GTP cyclohydrolase FolE2
C: GTP cyclohydrolase FolE2
D: GTP cyclohydrolase FolE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,20111
Polymers135,2454
Non-polymers9567
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-77 kcal/mol
Surface area37410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.314, 71.319, 193.018
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
GTP cyclohydrolase FolE2


Mass: 33811.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: folE2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A069BB45, GTP cyclohydrolase I

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Non-polymers , 5 types, 48 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#5: Chemical ChemComp-ZS9 / dehydrocostus lactone, bound form


Mass: 232.318 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H20O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.77 Å3/Da / Density % sol: 30.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium chloride, 0.1 M Bis-Tris, 1.3-1.7 M ammonium sulfate, 0.01 M cadmium chloride
PH range: 6.3-6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.1→48.25 Å / Num. obs: 17590 / % possible obs: 96.85 % / Redundancy: 9.8 % / Biso Wilson estimate: 62.65 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.2474 / Rpim(I) all: 0.07916 / Rrim(I) all: 0.2606 / Net I/σ(I): 10.13
Reflection shellResolution: 3.1→3.211 Å / Redundancy: 10 % / Rmerge(I) obs: 1.149 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 1716 / CC1/2: 0.834 / CC star: 0.954 / Rpim(I) all: 0.3566 / Rrim(I) all: 1.206 / % possible all: 97.55

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000v721.3data reduction
HKL-2000v721.3data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→47.16 Å / SU ML: 0.5291 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3119 875 5.01 %
Rwork0.2882 16607 -
obs0.2895 17482 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.62 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6730 0 13 41 6784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00946876
X-RAY DIFFRACTIONf_angle_d1.32959450
X-RAY DIFFRACTIONf_chiral_restr0.09111162
X-RAY DIFFRACTIONf_plane_restr0.00841241
X-RAY DIFFRACTIONf_dihedral_angle_d15.50312194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.290.37241390.3312724X-RAY DIFFRACTION97.25
3.29-3.550.34411490.32142712X-RAY DIFFRACTION96.85
3.55-3.910.39351400.31252710X-RAY DIFFRACTION96.51
3.91-4.470.23991410.27322745X-RAY DIFFRACTION96.23
4.47-5.630.28331500.25312770X-RAY DIFFRACTION96.95
5.63-47.160.30981560.28592946X-RAY DIFFRACTION97.58

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