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- PDB-2qv6: GTP cyclohydrolase III from M. jannaschii (MJ0145) complexed with... -

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Basic information

Entry
Database: PDB / ID: 2qv6
TitleGTP cyclohydrolase III from M. jannaschii (MJ0145) complexed with GTP and metal ions
ComponentsGTP cyclohydrolase III
KeywordsHYDROLASE / enzyme / GTP / FAPy
Function / homology
Function and homology information


GTP cyclohydrolase IIa / GTP cyclohydrolase IIa activity / biosynthetic process / GTP binding
Similarity search - Function
GTP cyclohydrolase III / GTP cyclohydrolase III / Nucleotide cyclase, GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / GTP cyclohydrolase III
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2 Å
AuthorsRoberts, S.A. / Bandarian, V.
CitationJournal: Biochemistry / Year: 2008
Title: A New Use for a Familiar Fold: The X-ray Crystal Structure of GTP-Bound GTP Cyclohydrolase III from Methanocaldococcus jannaschii Reveals a Two Metal Ion Catalytic Mechanism
Authors: Morrison, S.D. / Roberts, S.A. / Zegeer, A.M. / Montfort, W.R. / Bandarian, V.
History
DepositionAug 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)123,77220
Polymers121,2704
Non-polymers2,50116
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.203, 129.578, 90.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
GTP cyclohydrolase III / E.C.3.5.4.29 / MJ0145 / MjGC


Mass: 30317.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: gch3 / Plasmid: PET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57609, GTP cyclohydrolase IIa

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Non-polymers , 5 types, 209 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 11, 2007 / Details: confocal blue
RadiationMonochromator: confocal blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→31.3 Å / Num. obs: 76172 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.9 / Num. unique all: 7350 / % possible all: 92.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
REFMAC5.3refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→31.31 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.984 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24431 3845 5.1 %RANDOM
Rwork0.20632 ---
obs0.20829 72282 94.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.675 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--2.11 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8049 0 140 193 8382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228313
X-RAY DIFFRACTIONr_bond_other_d0.0010.025471
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.98411291
X-RAY DIFFRACTIONr_angle_other_deg0.979313424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95451016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07525.3400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.032151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9421545
X-RAY DIFFRACTIONr_chiral_restr0.0860.21294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021582
X-RAY DIFFRACTIONr_nbd_refined0.2320.21583
X-RAY DIFFRACTIONr_nbd_other0.1960.25343
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23965
X-RAY DIFFRACTIONr_nbtor_other0.0860.24371
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1510.240
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0820.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6661.55036
X-RAY DIFFRACTIONr_mcbond_other0.141.52060
X-RAY DIFFRACTIONr_mcangle_it1.24728154
X-RAY DIFFRACTIONr_scbond_it2.06333330
X-RAY DIFFRACTIONr_scangle_it3.2454.53137
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 265 -
Rwork0.376 5150 -
obs--92.63 %

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