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- PDB-1is8: Crystal structure of rat GTPCHI/GFRP stimulatory complex plus Zn -

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Basic information

Entry
Database: PDB / ID: 1is8
TitleCrystal structure of rat GTPCHI/GFRP stimulatory complex plus Zn
Components(GTP Cyclohydrolase ...) x 2
KeywordsHYDROLASE/PROTEIN BINDING / ENZYME-REGULATORY PROTEIN COMPLEX / HYDROLASE-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


dihydrobiopterin metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / intracellular protein-containing complex / GTP cyclohydrolase binding / GTP cyclohydrolase I regulator activity / pteridine-containing compound biosynthetic process / negative regulation of biosynthetic process / regulation of lung blood pressure / GTP cyclohydrolase I / GTP cyclohydrolase I activity ...dihydrobiopterin metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / intracellular protein-containing complex / GTP cyclohydrolase binding / GTP cyclohydrolase I regulator activity / pteridine-containing compound biosynthetic process / negative regulation of biosynthetic process / regulation of lung blood pressure / GTP cyclohydrolase I / GTP cyclohydrolase I activity / neuromuscular process controlling posture / regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / GTP-dependent protein binding / mitogen-activated protein kinase binding / negative regulation of cardiac muscle cell apoptotic process / response to pain / dopamine biosynthetic process / amino acid binding / response to tumor necrosis factor / negative regulation of cellular senescence / response to type II interferon / tetrahydrofolate biosynthetic process / positive regulation of heart rate / negative regulation of blood pressure / positive regulation of telomere maintenance via telomerase / regulation of blood pressure / vasodilation / melanosome / positive regulation of neuron apoptotic process / protein-containing complex assembly / cytoplasmic vesicle / nuclear membrane / response to lipopolysaccharide / GTPase activity / dendrite / calcium ion binding / GTP binding / protein-containing complex binding / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / 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) / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I signature 2. / GTP cyclohydrolase I / GTP cyclohydrolase I, conserved site / GTP cyclohydrolase I domain ...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) / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I signature 2. / GTP cyclohydrolase I / GTP cyclohydrolase I, conserved site / GTP cyclohydrolase I domain / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I / GTP cyclohydrolase I signature 1. / GTP Cyclohydrolase I; Chain A, domain 1 / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / PHENYLALANINE / GTP cyclohydrolase 1 / GTP cyclohydrolase 1 feedback regulatory protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsMaita, N. / Okada, K. / Hatakeyama, K. / Hakoshima, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal structure of the stimulatory complex of GTP cyclohydrolase I and its feedback regulatory protein GFRP.
Authors: Maita, N. / Okada, K. / Hatakeyama, K. / Hakoshima, T.
History
DepositionNov 18, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 I
B: GTP Cyclohydrolase I
C: GTP Cyclohydrolase I
D: GTP Cyclohydrolase I
E: GTP Cyclohydrolase I
F: GTP Cyclohydrolase I
G: GTP Cyclohydrolase I
H: GTP Cyclohydrolase I
I: GTP Cyclohydrolase I
J: GTP Cyclohydrolase I
K: GTP Cyclohydrolase I Feedback Regulatory Protein
L: GTP Cyclohydrolase I Feedback Regulatory Protein
M: GTP Cyclohydrolase I Feedback Regulatory Protein
N: GTP Cyclohydrolase I Feedback Regulatory Protein
O: GTP Cyclohydrolase I Feedback Regulatory Protein
P: GTP Cyclohydrolase I Feedback Regulatory Protein
Q: GTP Cyclohydrolase I Feedback Regulatory Protein
R: GTP Cyclohydrolase I Feedback Regulatory Protein
S: GTP Cyclohydrolase I Feedback Regulatory Protein
T: GTP Cyclohydrolase I Feedback Regulatory Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,72650
Polymers355,02920
Non-polymers2,69730
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area78600 Å2
ΔGint-803 kcal/mol
Surface area92460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.900, 111.430, 125.910
Angle α, β, γ (deg.)90.00, 97.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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GTP Cyclohydrolase ... , 2 types, 20 molecules ABCDEFGHIJKLMNOPQRST

#1: Protein
GTP Cyclohydrolase I


Mass: 25819.672 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pMALc / Production host: Escherichia coli (E. coli) / References: UniProt: P22288, GTP cyclohydrolase I
#2: Protein
GTP Cyclohydrolase I Feedback Regulatory Protein


Mass: 9683.225 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: P70552

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Non-polymers , 4 types, 401 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C9H11NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal grow
*PLUS
Method: vapor diffusion / Details: Maita, N., (2001) Acta Crystallogr., D57, 1153.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
224 %(v/v)MPD1reservoir
375 mMTris-HCl1reservoirpH7.5
450 mM1reservoirKCl
55 mMphenylalanine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.2818 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2001
RadiationMonochromator: Si(111) DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2818 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 93244 / Num. obs: 93244 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 57.2 Å2 / Rsym value: 0.095 / Net I/σ(I): 5.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 13544 / Rsym value: 0.286 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 693751 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
Lowest resolution: 2.84 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.286

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→15 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4662 5.02 %RANDOM
Rwork0.219 ---
all-92799 --
obs-92799 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22000 0 140 371 22511
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.347
X-RAY DIFFRACTIONc_bond_d0.0076
X-RAY DIFFRACTIONc_dihedral_angle_d23.31
X-RAY DIFFRACTIONc_improper_angle_d0.806
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.216 / Rfactor Rfree: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0082
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.31
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.806

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