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- PDB-8g8v: GTP Cyclohydrolase-IB with sodium -

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Basic information

Entry
Database: PDB / ID: 8g8v
TitleGTP Cyclohydrolase-IB with sodium
ComponentsGTP cyclohydrolase FolE2
KeywordsHYDROLASE / Cyclohydrolase / magnesium / GTP / fole2
Function / homologyTRIETHYLENE GLYCOL / SULFITE ION / :
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsMcWhorter, K.L. / Jhunjhunwala, R. / Davis, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM147557 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Combatting melioidosis with chemical synthetic lethality.
Authors: Zhang, Y. / McWhorter, K.L. / Rosen, P.C. / Klaus, J.R. / Gallant, E. / Amaya Lopez, C.Y. / Jhunjhunwala, R. / Chandler, J.R. / Davis, K.M. / Seyedsayamdost, M.R.
History
DepositionFeb 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,10619
Polymers67,6872
Non-polymers1,41917
Water3,351186
1
A: GTP cyclohydrolase FolE2
B: GTP cyclohydrolase FolE2
hetero molecules

A: GTP cyclohydrolase FolE2
B: GTP cyclohydrolase FolE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,21238
Polymers135,3734
Non-polymers2,83934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area24560 Å2
ΔGint-66 kcal/mol
Surface area34800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.499, 116.499, 70.806
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GTP cyclohydrolase FolE2


Mass: 33843.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: folE2, BURPS406E_D0599 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8ENW0, GTP cyclohydrolase I

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Non-polymers , 6 types, 203 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES Na, 1.6 M ammonium sulfate, 2% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.03→41.08 Å / Num. obs: 36073 / % possible obs: 99.93 % / Redundancy: 19.8 % / Biso Wilson estimate: 38.16 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.2366 / Rpim(I) all: 0.0546 / Rrim(I) all: 0.2429 / Net I/σ(I): 13.5
Reflection shellResolution: 2.03→2.103 Å / Redundancy: 17 % / Rmerge(I) obs: 1.719 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 3546 / CC1/2: 0.826 / CC star: 0.951 / Rpim(I) all: 0.4239 / Rrim(I) all: 1.771 / % possible all: 99.77

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→41.08 Å / SU ML: 0.2493 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4809
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2277 1810 5.02 %
Rwork0.1993 34258 -
obs0.2012 36064 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.62 Å2
Refinement stepCycle: LAST / Resolution: 2.03→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 86 186 4183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01284088
X-RAY DIFFRACTIONf_angle_d1.66945537
X-RAY DIFFRACTIONf_chiral_restr0.0946649
X-RAY DIFFRACTIONf_plane_restr0.0063710
X-RAY DIFFRACTIONf_dihedral_angle_d12.6191502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.2981350.27952598X-RAY DIFFRACTION99.78
2.08-2.150.31391380.24552604X-RAY DIFFRACTION99.96
2.15-2.220.25071390.24392607X-RAY DIFFRACTION100
2.22-2.290.23831350.2262595X-RAY DIFFRACTION99.96
2.29-2.390.26471380.22882619X-RAY DIFFRACTION100
2.39-2.50.28071350.23952613X-RAY DIFFRACTION100
2.5-2.630.23411380.23042648X-RAY DIFFRACTION100
2.63-2.790.23351420.22662608X-RAY DIFFRACTION100
2.79-3.010.23921370.2182636X-RAY DIFFRACTION100
3.01-3.310.26351420.20982632X-RAY DIFFRACTION99.96
3.31-3.790.21731380.17812659X-RAY DIFFRACTION100
3.79-4.770.18131400.16262671X-RAY DIFFRACTION100
4.77-41.080.21461530.18852768X-RAY DIFFRACTION99.97

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