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- PDB-1wur: Structure of GTP cyclohydrolase I Complexed with 8-oxo-dGTP -

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Basic information

Entry
Database: PDB / ID: 1wur
TitleStructure of GTP cyclohydrolase I Complexed with 8-oxo-dGTP
ComponentsGTP cyclohydrolase I
KeywordsHYDROLASE / BETA BARREL / PROTEIN-INHIBITOR COMPLEX / PTERIDINE / TETRAHYDROBIOPTERIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


GTP cyclohydrolase I / GTP cyclohydrolase I activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / GTP binding / zinc ion binding
Similarity search - Function
GTP cyclohydrolase I, N-terminal domain / 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, N-terminal domain / 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
8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / GTP cyclohydrolase 1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsTanaka, Y. / Nakagawa, N. / Masui, R. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biochem.(Tokyo) / Year: 2005
Title: Novel reaction mechanism of GTP cyclohydrolase I. High-resolution X-ray crystallography of Thermus thermophilus HB8 enzyme complexed with a transition state analogue, the 8-oxoguanine derivative
Authors: Tanaka, Y. / Nakagawa, N. / Kuramitsu, S. / Yokoyama, S. / Masui, R.
History
DepositionDec 8, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,80015
Polymers122,8575
Non-polymers2,94310
Water7,512417
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)251,59930
Polymers245,71310
Non-polymers5,88620
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area58850 Å2
ΔGint-633 kcal/mol
Surface area56730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)160.570, 110.560, 70.530
Angle α, β, γ (deg.)90.00, 105.78, 90.00
Int Tables number5
Space group name H-MC121
DetailsBiological unit is a decamer generated from the symmetry operation with asymmetrical unit: (-x, y, -z)

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Components

#1: Protein
GTP cyclohydrolase I


Mass: 24571.332 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SH52, 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-8DG / 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 3.4% PEG400, 0.1M HEPES, 2.0M Ammonium sulfate, 15% glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.979 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 28, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 103478 / Num. obs: 103478 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25
Reflection shellResolution: 1.82→1.89 Å / % possible all: 98.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→46.69 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.237 9983 RANDOM
Rwork0.206 --
all-99268 -
obs-99268 -
Refinement stepCycle: LAST / Resolution: 1.82→46.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7326 0 165 417 7908

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