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- PDB-1sql: Crystal structure of 7,8-dihydroneopterin aldolase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 1sql
TitleCrystal structure of 7,8-dihydroneopterin aldolase in complex with guanine
Componentsdihydroneopterin aldolase
KeywordsLYASE / tetrahydrofolate biosynthesis / aldolase classes / retroaldol reaction / purin binding / Schiff base
Function / homology
Function and homology information


dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid-containing compound metabolic process / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / cytoplasm / cytosol
Similarity search - Function
Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / 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 / Alpha Beta
Similarity search - Domain/homology
GUANINE / Dihydroneopterin aldolase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBauer, S. / Schott, A.K. / Illarionova, V. / Bacher, A. / Huber, R. / Fischer, M.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Biosynthesis of Tetrahydrofolate in Plants: Crystal Structure of 7,8-Dihydroneopterin Aldolase from Arabidopsis thaliana Reveals a Novel Adolase Class.
Authors: Bauer, S. / Schott, A.K. / Illarionova, V. / Bacher, A. / Huber, R. / Fischer, M.
History
DepositionMar 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: dihydroneopterin aldolase
B: dihydroneopterin aldolase
C: dihydroneopterin aldolase
D: dihydroneopterin aldolase
E: dihydroneopterin aldolase
F: dihydroneopterin aldolase
G: dihydroneopterin aldolase
H: dihydroneopterin aldolase
I: dihydroneopterin aldolase
J: dihydroneopterin aldolase
K: dihydroneopterin aldolase
L: dihydroneopterin aldolase
M: dihydroneopterin aldolase
N: dihydroneopterin aldolase
O: dihydroneopterin aldolase
P: dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,26032
Polymers260,84216
Non-polymers2,41816
Water16,736929
1
A: dihydroneopterin aldolase
B: dihydroneopterin aldolase
C: dihydroneopterin aldolase
D: dihydroneopterin aldolase
E: dihydroneopterin aldolase
F: dihydroneopterin aldolase
G: dihydroneopterin aldolase
H: dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,63016
Polymers130,4218
Non-polymers1,2098
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24690 Å2
ΔGint-94 kcal/mol
Surface area36420 Å2
MethodPISA
2
I: dihydroneopterin aldolase
J: dihydroneopterin aldolase
K: dihydroneopterin aldolase
L: dihydroneopterin aldolase
M: dihydroneopterin aldolase
N: dihydroneopterin aldolase
O: dihydroneopterin aldolase
P: dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,63016
Polymers130,4218
Non-polymers1,2098
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24630 Å2
ΔGint-96 kcal/mol
Surface area36770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.55, 84.22, 89.05
Angle α, β, γ (deg.)90.14, 89.99, 76.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
dihydroneopterin aldolase


Mass: 16302.626 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: M15[pREP4] / References: UniProt: Q9SF23
#2: Chemical
ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C5H5N5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 929 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: Tris, PEG 2000 MME, C-HEGA-11, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 17, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 86882 / % possible obs: 95.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.09
Reflection shellResolution: 2.2→2.28 Å / % possible obs: 92.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.03

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DHN

1dhn


Resolution: 2.2→20 Å
RfactorNum. reflection
Rfree0.26 3837
Rwork0.204 -
obs-82949
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15295 0 176 929 16400

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