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- PDB-3q11: Crystals Structure of Aspartate beta-Semialdehyde Dehydrogenase f... -

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Basic information

Entry
Database: PDB / ID: 3q11
TitleCrystals Structure of Aspartate beta-Semialdehyde Dehydrogenase from Streptococcus pneumoniae with NADP and aspartyl beta-difluorophosphonate
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / NADP / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 5,5-difluoro-4-oxo-5-phosphono-D-norvaline / :
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsPavlovsky, A.G. / Viola, R.E. / Faehnle, C.R.
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 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,39112
Polymers80,0772
Non-polymers2,31410
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-21 kcal/mol
Surface area25310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.014, 98.702, 64.528
Angle α, β, γ (deg.)90.00, 100.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aspartate-semialdehyde dehydrogenase


Mass: 40038.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: CGSSp23BS72_03388 / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 (de3)
References: UniProt: A5MTN0, aspartate-semialdehyde dehydrogenase

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Non-polymers , 5 types, 619 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-P4F / 5,5-difluoro-4-oxo-5-phosphono-D-norvaline


Type: D-peptide linking / Mass: 247.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8F2NO6P
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12 % PEG 3350, 0.1 M ammonium acetate, 0.05 M Na-citrate buffer, 10mM DTT, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: confocal mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→37.8 Å / Num. obs: 68322 / % possible obs: 89 % / Redundancy: 1.98 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.067 / Net I/σ(I): 6.8
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 1.6 / Num. unique all: 3647 / Rsym value: 0 / % possible all: 89.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
REFMAC5.5.0102refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→37.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.453 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24177 3095 5.1 %RANDOM
Rwork0.20306 ---
obs0.20502 57723 88.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.035 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.72 Å2
2--1.54 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5456 0 147 609 6212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225723
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.9927793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12625.043232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27315955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5191526
X-RAY DIFFRACTIONr_chiral_restr0.0720.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214224
X-RAY DIFFRACTIONr_mcbond_it0.2881.53581
X-RAY DIFFRACTIONr_mcangle_it0.55725791
X-RAY DIFFRACTIONr_scbond_it0.94732142
X-RAY DIFFRACTIONr_scangle_it1.5754.52001
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 236 -
Rwork0.391 4264 -
obs--88.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3212-0.0747-0.34430.07520.17181.3705-0.0326-0.023-0.0173-0.0121-0.01910.0264-0.09730.00310.05180.0388-0.0092-0.02490.0582-0.0080.04673.415-0.4087.945
20.1637-0.1252-0.28980.15980.03861.69370.001-0.0363-0.0308-0.0449-0.05420.02820.15860.32440.05320.0560.0321-0.01580.12690.01510.036922.826-10.74-20.677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 359
2X-RAY DIFFRACTION1A367 - 372
3X-RAY DIFFRACTION1A373 - 849
4X-RAY DIFFRACTION2B2 - 358
5X-RAY DIFFRACTION2B367 - 370
6X-RAY DIFFRACTION2B371 - 851

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