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- PDB-1jg5: CRYSTAL STRUCTURE OF RAT GTP CYCLOHYDROLASE I FEEDBACK REGULATORY... -

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Basic information

Entry
Database: PDB / ID: 1jg5
TitleCRYSTAL STRUCTURE OF RAT GTP CYCLOHYDROLASE I FEEDBACK REGULATORY PROTEIN, GFRP
ComponentsGTP CYCLOHYDROLASE I FEEDBACK REGULATORY PROTEIN
KeywordsPROTEIN BINDING / alpha/beta structure / beta sheet
Function / homology
Function and homology information


Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / intracellular protein-containing complex / GTP cyclohydrolase binding / GTP cyclohydrolase I regulator activity / negative regulation of biosynthetic process / GTP-dependent protein binding / amino acid binding / melanosome / protein-containing complex assembly / nuclear membrane ...Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / intracellular protein-containing complex / GTP cyclohydrolase binding / GTP cyclohydrolase I regulator activity / negative regulation of biosynthetic process / GTP-dependent protein binding / amino acid binding / melanosome / protein-containing complex assembly / nuclear membrane / dendrite / protein-containing complex binding / protein-containing complex / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Gtp Cyclohydrolase I Feedback Regulatory Protein; Chain: K / GTP cyclohydrolase I feedback regulatory protein GFRP / GTP cyclohydrolase I, feedback regulatory protein / GFRP superfamily / GTP cyclohydrolase I feedback regulatory protein (GFRP) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / GTP cyclohydrolase 1 feedback regulatory protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.6 Å
AuthorsBader, G. / Schiffmann, S. / Herrmann, A. / Fischer, M. / Gutlich, M. / Auerbach, G. / Ploom, T. / Bacher, A. / Huber, R. / Lemm, T.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of rat GTP cyclohydrolase I feedback regulatory protein, GFRP.
Authors: Bader, G. / Schiffmann, S. / Herrmann, A. / Fischer, M. / Gutlich, M. / Auerbach, G. / Ploom, T. / Bacher, A. / Huber, R. / Lemm, T.
History
DepositionJun 23, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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_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.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_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_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

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Assembly

Deposited unit
A: GTP CYCLOHYDROLASE I FEEDBACK REGULATORY PROTEIN
B: GTP CYCLOHYDROLASE I FEEDBACK REGULATORY PROTEIN
C: GTP CYCLOHYDROLASE I FEEDBACK REGULATORY PROTEIN
D: GTP CYCLOHYDROLASE I FEEDBACK REGULATORY PROTEIN
E: GTP CYCLOHYDROLASE I FEEDBACK REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,95610
Polymers47,7605
Non-polymers1955
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint-72 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.803, 110.052, 38.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
GTP CYCLOHYDROLASE I FEEDBACK REGULATORY PROTEIN


Mass: 9552.030 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PQE(7) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 / References: UniProt: P70552
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293 K / Method: batch crystallization / pH: 7.4
Details: 100mM potassium phosphate, 2mM DTT, pH 7.4, batch crystallization, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMpotassium phosphate11
22 mMdithiothreitol11
35 mg/mlprotein11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→35 Å / Num. obs: 14791 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.118
Reflection shellResolution: 2.6→2.65 Å
Reflection
*PLUS
Lowest resolution: 35 Å / Num. measured all: 154398

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Processing

Software
NameVersionClassification
PROTEINmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
PROTEINphasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 715 -random
Rwork0.166 ---
all-14659 --
obs-14070 96 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.7 Å20 Å20 Å2
2---4.9 Å20 Å2
3----2.8 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 5 256 3601
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.38
X-RAY DIFFRACTIONc_angle_d0.007
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / σ(F): 2 / Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.38

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