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- PDB-1rs2: DHNA complex with 8-Amino-1,3-dimethyl-3,7-dihydropurine-2,6-dione -

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Basic information

Entry
Database: PDB / ID: 1rs2
TitleDHNA complex with 8-Amino-1,3-dimethyl-3,7-dihydropurine-2,6-dione
ComponentsDihydroneopterin aldolase
KeywordsLYASE / DHNA / 7 / 8-Dihydroneop8-Amino-1 / 3-dimethyl-3 / 7-dihydropurine-2 / 6-dioneterin Aldolase
Function / homology
Function and homology information


7,8-dihydroneopterin epimerase / dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / isomerase activity / tetrahydrofolate biosynthetic process
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
8-AMINO-1,3-DIMETHYL-3,7-DIHYDROPURINE-2,6-DIONE / Dihydroneopterin aldolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.31 Å
AuthorsSanders, W.J. / Nienaber, V.L. / Lerner, C.G. / McCall, J.O. / Merrick, S.M. / Swanson, S.J. / Harlan, J.E. / Stoll, V.S. / Stamper, G.F. / Betz, S.F. ...Sanders, W.J. / Nienaber, V.L. / Lerner, C.G. / McCall, J.O. / Merrick, S.M. / Swanson, S.J. / Harlan, J.E. / Stoll, V.S. / Stamper, G.F. / Betz, S.F. / Condroski, K.R. / Meadows, R.P. / Severin, J.M. / Walter, K.A. / Magdalinos, P. / Jakob, C.G. / Wagner, R. / Beutel, B.A.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Discovery of Potent Inhibitors of Dihydroneopterin Aldolase Using CrystaLEAD High-Throughput X-ray Crystallographic Screening and Structure-Directed Lead Optimization.
Authors: Sanders, W.J. / Nienaber, V.L. / Lerner, C.G. / McCall, J.O. / Merrick, S.M. / Swanson, S.J. / Harlan, J.E. / Stoll, V.S. / Stamper, G.F. / Betz, S.F. / Condroski, K.R. / Meadows, R.P. / ...Authors: Sanders, W.J. / Nienaber, V.L. / Lerner, C.G. / McCall, J.O. / Merrick, S.M. / Swanson, S.J. / Harlan, J.E. / Stoll, V.S. / Stamper, G.F. / Betz, S.F. / Condroski, K.R. / Meadows, R.P. / Severin, J.M. / Walter, K.A. / Magdalinos, P. / Jakob, C.G. / Wagner, R. / Beutel, B.A.
History
DepositionDec 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,7701
Non-polymers1951
Water21612
1
A: Dihydroneopterin aldolase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)111,71916
Polymers110,1578
Non-polymers1,5618
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area25430 Å2
ΔGint-99 kcal/mol
Surface area36110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.947, 60.947, 123.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Dihydroneopterin aldolase / / DHNA


Mass: 13769.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: FOLB / Production host: Escherichia coli (E. coli) / References: UniProt: P56740, dihydroneopterin aldolase
#2: Chemical ChemComp-209 / 8-AMINO-1,3-DIMETHYL-3,7-DIHYDROPURINE-2,6-DIONE


Mass: 195.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.08 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Ammonium Acetate, 0.1M tri-sodium citrate pH 5.6, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.31→34.15 Å / Num. obs: 4595 / % possible obs: 84.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.2 Å2
Reflection shellResolution: 2.31→2.44 Å / % possible all: 70.3

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Processing

Software
NameVersionClassification
CNX2000refinement
HKL-2000data reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.31→34.15 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 145080.62 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.311 483 10.5 %RANDOM
Rwork0.265 ---
obs-4595 84.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.0909072 e/Å3
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20 Å20 Å2
2--2.36 Å20 Å2
3----4.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.31→34.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 14 12 993
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.63
LS refinement shellResolution: 2.31→2.44 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.415 77 12.3 %
Rwork0.341 550 -
obs-9815 70.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMLIG.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4LIG.PAR

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