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- PDB-1rry: DHNA complexed with 2-amino-4-hydroxy-5-carboxyethylpyrimidine -

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Basic information

Entry
Database: PDB / ID: 1rry
TitleDHNA complexed with 2-amino-4-hydroxy-5-carboxyethylpyrimidine
ComponentsDihydroneopterin aldolase
KeywordsLYASE / DHNA / 2-amino-4-hydroxy-5-carboxyethylpyrimidine
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
Chem-204 / Dihydroneopterin aldolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.7 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

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Assembly

Deposited unit
A: Dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9532
Polymers13,7701
Non-polymers1831
Water0
1
A: Dihydroneopterin aldolase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)111,62216
Polymers110,1578
Non-polymers1,4658
Water0
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 area25490 Å2
ΔGint-96 kcal/mol
Surface area35810 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-204 / 2-AMINO-4-HYDROXYPYRIMIDINE-5-CARBOXYLIC ACID ETHYL ESTER


Mass: 183.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N3O3

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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: 0.2 M Ammonium Acetate, 0.1 M 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: 2.7→35.56 Å / Num. all: 10505 / Num. obs: 2816 / % possible obs: 81.4 % / Biso Wilson estimate: 38.7 Å2
Reflection shellResolution: 2.7→2.87 Å / % possible all: 85.4

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Processing

Software
NameVersionClassification
CNX2000refinement
HKL-2000data reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→35.36 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 273047.96 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.305 302 10.7 %RANDOM
Rwork0.229 ---
all-10505 --
obs-2816 81.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.06409162 e/Å3
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å20 Å2
2--1.59 Å20 Å2
3----3.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.7→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 13 0 980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 53 11.3 %
Rwork0.289 415 -
obs-10505 85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM104.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4104.PAR

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