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- PDB-1n3r: Biosynthesis of pteridins. Reaction mechanism of GTP cyclohydrolase I -

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Basic information

Entry
Database: PDB / ID: 1n3r
TitleBiosynthesis of pteridins. Reaction mechanism of GTP cyclohydrolase I
ComponentsGTP cyclohydrolase I
KeywordsHYDROLASE / Biosynthesis / folic acid / GTP cyclohydrolase I / tetrahydropterin / pteridines
Function / homology
Function and homology information


GTP cyclohydrolase I / GTP cyclohydrolase I activity / : / tetrahydrobiopterin biosynthetic process / queuosine biosynthetic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / GTP binding / protein-containing complex / zinc ion binding ...GTP cyclohydrolase I / GTP cyclohydrolase I activity / : / tetrahydrobiopterin biosynthetic process / queuosine biosynthetic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / GTP binding / protein-containing complex / zinc ion binding / identical protein binding / 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
GUANOSINE-5'-TRIPHOSPHATE / GTP cyclohydrolase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRebelo, J. / Auerbach, G. / Bader, G. / Bracher, A. / Nar, H. / Hoesl, C. / Schramek, N. / Kaiser, J. / Bacher, A. / Huber, R. / Fischer, M.
CitationJournal: J.MOL.BIOL. / Year: 2003
Title: Biosynthesis of Pteridines. Reaction Mechanism of GTP Cyclohydrolase I
Authors: Rebelo, J. / Auerbach, G. / Bader, G. / Bracher, A. / Nar, H. / Hoesl, C. / Schramek, N. / Kaiser, J. / Bacher, A. / Huber, R. / Fischer, M.
History
DepositionOct 29, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
L: GTP cyclohydrolase I
M: GTP cyclohydrolase I
N: GTP cyclohydrolase I
O: GTP cyclohydrolase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,08330
Polymers370,23615
Non-polymers7,84815
Water1,42379
1
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)126,02810
Polymers123,4125
Non-polymers2,6165
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16110 Å2
ΔGint-14 kcal/mol
Surface area51210 Å2
MethodPISA
2
F: GTP cyclohydrolase I
G: GTP cyclohydrolase I
H: GTP cyclohydrolase I
I: GTP cyclohydrolase I
J: GTP cyclohydrolase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,02810
Polymers123,4125
Non-polymers2,6165
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16070 Å2
ΔGint-9 kcal/mol
Surface area51930 Å2
MethodPISA
3
K: GTP cyclohydrolase I
L: GTP cyclohydrolase I
M: GTP cyclohydrolase I
N: GTP cyclohydrolase I
O: GTP cyclohydrolase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,02810
Polymers123,4125
Non-polymers2,6165
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16090 Å2
ΔGint-9 kcal/mol
Surface area51880 Å2
MethodPISA
4
A: GTP cyclohydrolase I
B: GTP cyclohydrolase I
C: GTP cyclohydrolase I
D: GTP cyclohydrolase I
E: GTP cyclohydrolase I
hetero molecules

F: GTP cyclohydrolase I
G: GTP cyclohydrolase I
H: GTP cyclohydrolase I
I: GTP cyclohydrolase I
J: GTP cyclohydrolase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,05620
Polymers246,82410
Non-polymers5,23210
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x+1/2,-y+1/2,-z1
Buried area60580 Å2
ΔGint-173 kcal/mol
Surface area74740 Å2
MethodPISA
5
K: GTP cyclohydrolase I
L: GTP cyclohydrolase I
M: GTP cyclohydrolase I
N: GTP cyclohydrolase I
O: GTP cyclohydrolase I
hetero molecules

K: GTP cyclohydrolase I
L: GTP cyclohydrolase I
M: GTP cyclohydrolase I
N: GTP cyclohydrolase I
O: GTP cyclohydrolase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,05620
Polymers246,82410
Non-polymers5,23210
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area60770 Å2
ΔGint-162 kcal/mol
Surface area75180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.466, 313.258, 130.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
GTP cyclohydrolase I /


Mass: 24682.381 Da / Num. of mol.: 15 / Mutation: H112S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pNC0 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6T5, GTP cyclohydrolase I
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: Peg 6000, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 10, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 2178312 / Num. obs: 105682 / % possible obs: 97.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272 5284 RANDOM
Rwork0.218 --
all0.222 2178312 -
obs0.221 105682 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25912 0 480 79 26471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.51

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