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- PDB-8g6c: GTP Cyclohydrolase-IB with manganese -

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Basic information

Entry
Database: PDB / ID: 8g6c
TitleGTP Cyclohydrolase-IB with manganese
ComponentsGTP cyclohydrolase FolE2
KeywordsHYDROLASE / Cyclohydrolase / GTP / manganese / fole2
Function / homology: / GTP cyclohydrolase FolE2/MptA / GTP cyclohydrolase FolE2 / Type I GTP cyclohydrolase folE2 / GTP cyclohydrolase I / GTP cyclohydrolase I activity / : / GTP cyclohydrolase FolE2
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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)R35-GM147557 United States
Citation
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionFeb 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,29113
Polymers67,6232
Non-polymers66811
Water68538
1
A: GTP cyclohydrolase FolE2
B: GTP cyclohydrolase FolE2
hetero molecules

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


  • defined by author&software
  • 137 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)136,58226
Polymers135,2454
Non-polymers1,33722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area20340 Å2
ΔGint-56 kcal/mol
Surface area35710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.522, 117.522, 72.073
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

#1: Protein GTP cyclohydrolase FolE2


Mass: 33811.340 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaCl, 0.1 M BIS TRIS, 1.3 - 1.7 M ammonium sulfate
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: Oct 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.82→41.57 Å / Num. obs: 14120 / % possible obs: 99.1 % / Redundancy: 20.6 % / Biso Wilson estimate: 47.92 Å2 / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.2693 / Rpim(I) all: 0.06028 / Rrim(I) all: 0.2761 / Net I/σ(I): 16.02
Reflection shellResolution: 2.82→2.921 Å / Redundancy: 13 % / Rmerge(I) obs: 1.397 / Mean I/σ(I) obs: 1.73 / Num. unique obs: 1357 / CC1/2: 0.672 / CC star: 0.896 / Rpim(I) all: 0.395 / Rrim(I) all: 1.453 / % possible all: 97.07

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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: 2.82→41.57 Å / SU ML: 0.3036 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0695
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2492 703 5.01 %
Rwork0.2139 13319 -
obs0.2157 14020 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.48 Å2
Refinement stepCycle: LAST / Resolution: 2.82→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3801 0 38 38 3877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113898
X-RAY DIFFRACTIONf_angle_d1.45245287
X-RAY DIFFRACTIONf_chiral_restr0.0866619
X-RAY DIFFRACTIONf_plane_restr0.0056689
X-RAY DIFFRACTIONf_dihedral_angle_d12.59071408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-3.040.3131320.28612599X-RAY DIFFRACTION97.64
3.04-3.340.29161420.24692615X-RAY DIFFRACTION99.24
3.34-3.830.2421400.21492660X-RAY DIFFRACTION99.5
3.83-4.820.2061420.18092679X-RAY DIFFRACTION99.86
4.82-41.570.25561470.20632766X-RAY DIFFRACTION99.52

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