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- PDB-4rl4: Crystal structure of GTP cyclohydrolase II from Helicobacter pylo... -

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Basic information

Entry
Database: PDB / ID: 4rl4
TitleCrystal structure of GTP cyclohydrolase II from Helicobacter pylori 26695
ComponentsGTP cyclohydrolase-2
KeywordsHYDROLASE / alpha/beta fold / DARP / Riboflavin
Function / homology
Function and homology information


GTP cyclohydrolase II / GTP cyclohydrolase II activity / riboflavin biosynthetic process / GTP binding / zinc ion binding / cytosol
Similarity search - Function
GTP cyclohydrolase II / GTP cyclohydrolase II, RibA / GTP cyclohydrolase II / GTP cyclohydrolase II superfamily / GTP cyclohydrolase II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE / GTP cyclohydrolase-2
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsYadav, S. / Karthikeyan, S.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural and biochemical characterization of GTP cyclohydrolase II from Helicobacter pylori reveals its redox dependent catalytic activity.
Authors: Yadav, S. / Karthikeyan, S.
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP cyclohydrolase-2
B: GTP cyclohydrolase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5594
Polymers48,2032
Non-polymers3562
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-30 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.283, 69.283, 179.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-314-

HOH

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Components

#1: Protein GTP cyclohydrolase-2 / GTP cyclohydrolase II


Mass: 24101.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: HP_0802, ribA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O08315, GTP cyclohydrolase II
#2: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium citrate tribasic, 15% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH range: 6.7-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 24, 2012
RadiationMonochromator: Varymax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.199→64.65 Å / Num. obs: 23212 / % possible obs: 96.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 33.1
Reflection shellResolution: 2.199→2.24 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.3 / Num. unique all: 831 / % possible all: 72.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BZ0

2bz0


Resolution: 2.199→64.65 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.173 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26048 1131 5.1 %RANDOM
Rwork0.21158 ---
all0.2116 ---
obs0.2139 21061 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.243 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å2-0 Å2
2--1.68 Å2-0 Å2
3----3.36 Å2
Refinement stepCycle: LAST / Resolution: 2.199→64.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 18 87 2777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192729
X-RAY DIFFRACTIONr_bond_other_d0.0010.022604
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9823667
X-RAY DIFFRACTIONr_angle_other_deg0.72835977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74824.297128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87615492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4391520
X-RAY DIFFRACTIONr_chiral_restr0.0680.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02627
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5384.5911380
X-RAY DIFFRACTIONr_mcbond_other2.5394.5891379
X-RAY DIFFRACTIONr_mcangle_it4.1666.8641718
X-RAY DIFFRACTIONr_mcangle_other4.1656.8661719
X-RAY DIFFRACTIONr_scbond_it3.0954.911349
X-RAY DIFFRACTIONr_scbond_other3.0724.8851341
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9577.1761937
X-RAY DIFFRACTIONr_long_range_B_refined7.69335.5042999
X-RAY DIFFRACTIONr_long_range_B_other7.65535.3982985
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 55 -
Rwork0.312 1213 -
obs--75.7 %

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