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- PDB-1fb1: CRYSTAL STRUCTURE OF HUMAN GTP CYCLOHYDROLASE I -

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Basic information

Entry
Database: PDB / ID: 1fb1
TitleCRYSTAL STRUCTURE OF HUMAN GTP CYCLOHYDROLASE I
ComponentsGTP CYCLOHYDROLASE I
KeywordsHYDROLASE / ALLOSTERIC ENZYME / PHOSPHORYLATION
Function / homology
Function and homology information


pteridine-containing compound biosynthetic process / regulation of lung blood pressure / GTP cyclohydrolase I / GTP cyclohydrolase I activity / : / neuromuscular process controlling posture / regulation of removal of superoxide radicals / GTP-dependent protein binding / tetrahydrobiopterin biosynthetic process / neuron projection terminus ...pteridine-containing compound biosynthetic process / regulation of lung blood pressure / GTP cyclohydrolase I / GTP cyclohydrolase I activity / : / neuromuscular process controlling posture / regulation of removal of superoxide radicals / GTP-dependent protein binding / tetrahydrobiopterin biosynthetic process / neuron projection terminus / dopamine biosynthetic process / mitogen-activated protein kinase binding / response to pain / positive regulation of heart rate / response to type II interferon / response to tumor necrosis factor / translation initiation factor binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / negative regulation of blood pressure / nitric oxide biosynthetic process / positive regulation of nitric-oxide synthase activity / regulation of blood pressure / vasodilation / cytoplasmic vesicle / protein-containing complex assembly / nuclear membrane / response to lipopolysaccharide / GTPase activity / calcium ion binding / protein-containing complex binding / GTP binding / protein homodimerization activity / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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, 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
ISOPROPYL ALCOHOL / GTP cyclohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsAuerbach, G. / Herrmann, A. / Bracher, A. / Bader, G. / Gutlich, M. / Fischer, M. / Neukamm, M. / Nar, H. / Garrido-Franco, M. / Richardson, J. ...Auerbach, G. / Herrmann, A. / Bracher, A. / Bader, G. / Gutlich, M. / Fischer, M. / Neukamm, M. / Nar, H. / Garrido-Franco, M. / Richardson, J. / Huber, R. / Bacher, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Zinc plays a key role in human and bacterial GTP cyclohydrolase I.
Authors: Auerbach, G. / Herrmann, A. / Bracher, A. / Bader, G. / Gutlich, M. / Fischer, M. / Neukamm, M. / Garrido-Franco, M. / Richardson, J. / Nar, H. / Huber, R. / Bacher, A.
History
DepositionJul 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 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_asym_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,15515
Polymers110,5275
Non-polymers62810
Water0
1
A: GTP CYCLOHYDROLASE I
B: GTP CYCLOHYDROLASE I
C: GTP CYCLOHYDROLASE I
D: GTP CYCLOHYDROLASE I
E: GTP CYCLOHYDROLASE I
hetero molecules

A: GTP CYCLOHYDROLASE I
B: GTP CYCLOHYDROLASE I
C: GTP CYCLOHYDROLASE I
D: GTP CYCLOHYDROLASE I
E: GTP CYCLOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,31030
Polymers221,05510
Non-polymers1,25520
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area50010 Å2
ΔGint-551 kcal/mol
Surface area68690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)115.110, 115.110, 387.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a decamer constructed by the pentamer by crystallographic symmetry

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Components

#1: Protein
GTP CYCLOHYDROLASE I / / GTP-CH-I


Mass: 22105.488 Da / Num. of mol.: 5 / Fragment: RESIDUES 55-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HOMO SAPIENS / Production host: Escherichia coli (E. coli) / References: UniProt: P30793, GTP cyclohydrolase I
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 9

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulphate, isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.6 mg/mlprotein1drop
2100 mMpotassium phosphate1drop
32 mM1,4-dithiothreitol1drop
40.02 %1dropNaN3
51.0 Mammonium sulfate1reservoir
63.2 %isopropanol1reservoir
72 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 3.1→14.97 Å / Num. all: 276288 / Num. obs: 25288 / % possible obs: 84.5 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.165
Reflection shellResolution: 3.1→3.29 Å / % possible all: 41.9
Reflection
*PLUS
Num. measured all: 276838
Reflection shell
*PLUS
% possible obs: 41.9 %

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 3.1→14.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3214433.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 2358 9.9 %RANDOM
Rwork0.204 ---
obs0.204 23825 84.2 %-
all-276838 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 136.5 Å2 / ksol: 0.215 e/Å3
Displacement parametersBiso mean: 93.9 Å2
Baniso -1Baniso -2Baniso -3
1-15.96 Å216.8 Å20 Å2
2--15.96 Å20 Å2
3----31.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 3.1→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7725 0 25 0 7750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 195 10.2 %
Rwork0.352 1714 -
obs--41.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_ISO.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4IPA_XPLOR_PAR.TXTIPA_XPLOR_TOP.TXT
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 88.68 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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