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- PDB-3pyl: Crystal structure of aspartate beta-semialdehide dehydrogenase fr... -

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Basic information

Entry
Database: PDB / ID: 3pyl
TitleCrystal structure of aspartate beta-semialdehide dehydrogenase from Streptococcus pneumoniae with D-2,3-diaminopropionate
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / NADP / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homologyDihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / 3-amino-D-alanine / :
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsPavlovsky, A.G. / Liu, X. / Faehnle, C.R. / Potente, N. / Viola, R.E.
CitationJournal: Chem.Biol.Drug Des. / Year: 2012
Title: Structural Characterization of Inhibitors with Selectivity against Members of a Homologous Enzyme Family.
Authors: Pavlovsky, A.G. / Liu, X. / Faehnle, C.R. / Potente, N. / Viola, R.E.
History
DepositionDec 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Non-polymer description
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Oct 15, 2014Group: Structure summary
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Assembly

Deposited unit
A: Aspartate-semialdehyde dehydrogenase
B: Aspartate-semialdehyde dehydrogenase
C: Aspartate-semialdehyde dehydrogenase
D: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,4667
Polymers160,1544
Non-polymers3123
Water9,998555
1
A: Aspartate-semialdehyde dehydrogenase
B: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2854
Polymers80,0772
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-21 kcal/mol
Surface area25310 Å2
MethodPISA
2
C: Aspartate-semialdehyde dehydrogenase
D: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1813
Polymers80,0772
Non-polymers1041
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-19 kcal/mol
Surface area26010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.115, 78.155, 246.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Aspartate-semialdehyde dehydrogenase


Mass: 40038.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: SP23-BS72 / Gene: CGSSp23BS72_03388 / Plasmid: pet 28a / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3)
References: UniProt: A5MTN0, aspartate-semialdehyde dehydrogenase
#2: Chemical ChemComp-2RA / 3-amino-D-alanine / diaminopropanoic acid


Type: D-peptide linking / Mass: 104.108 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 % PEG 3350, 0.1 M MES, 0.1 M ammonium acetate, 10 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.07 Å / Num. obs: 64822 / % possible obs: 90 % / Redundancy: 3.8 % / Biso Wilson estimate: 32.3 Å2 / Rsym value: 0.067 / Net I/σ(I): 18.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 5 / Num. unique all: 5748 / Rsym value: 0.191 / % possible all: 80.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→47.07 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.136 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3255 5 %RANDOM
Rwork0.19825 ---
obs0.20058 61536 89.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.64 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10879 0 21 555 11455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211114
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.96215106
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63651429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53625.152460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.054151884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3111548
X-RAY DIFFRACTIONr_chiral_restr0.0750.21771
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218294
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3851.57141
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.735211539
X-RAY DIFFRACTIONr_scbond_it1.12433973
X-RAY DIFFRACTIONr_scangle_it1.8964.53566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 201 -
Rwork0.282 3678 -
obs--73.62 %

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