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- PDB-4r5h: Crystal structure of sp-Aspartate-Semialdehyde-Dehydrogenase with... -

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Basic information

Entry
Database: PDB / ID: 4r5h
TitleCrystal structure of sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide-Adenine-Dinucleotide-Phosphate and 3-carboxy-propenyl-phthalic acid
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann Fold / NADP
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
Chem-3JN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsPavlovsky, A.G. / Thangavelu, B. / Bhansali, P. / Viola, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: A cautionary tale of structure-guided inhibitor development against an essential enzyme in the aspartate-biosynthetic pathway.
Authors: Pavlovsky, A.G. / Thangavelu, B. / Bhansali, P. / Viola, R.E.
History
DepositionAug 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,35715
Polymers80,0772
Non-polymers2,28013
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-22 kcal/mol
Surface area24440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.620, 97.565, 64.555
Angle α, β, γ (deg.)90.00, 100.39, 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 / ASA dehydrogenase / ASADH / Aspartate-beta-semialdehyde dehydrogenase


Mass: 40038.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NADP / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: SP23-BS72 / Gene: asd, CGSSp23BS72_03388 / Plasmid: pET28A / 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, 579 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-3JN / 3-[(1E)-3-carboxyprop-1-en-1-yl]benzene-1,2-dicarboxylic acid / 3-carboxy-propenyl-phthalic acid


Mass: 250.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O6
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15-22% PEG 3350, 0.1 M Na acetate, 0.1 M MES (pH6.5), 10 mM TCEP, 3% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 27, 2014 / Details: double crystal monochromator
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 67177 / Num. obs: 63953 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rsym value: 0.105 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.8-1.862.63.70.34197.5
3.88-502.89.20.087187.9
3.08-3.882.88.10.094193.1
2.69-3.082.86.50.113194.4
2.44-2.692.75.60.134195.8
2.27-2.442.75.10.152196.1
2.13-2.272.75.10.161196.6
2.03-2.132.750.188197.2
1.94-2.032.74.60.22196.7
1.86-1.942.64.20.261197.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4R3N

4r3n


Resolution: 1.8→63.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.13 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21272 3215 5 %RANDOM
Rwork0.18336 ---
obs0.18483 60868 95.46 %-
all-63755 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.702 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-1.32 Å2
2--2.31 Å20 Å2
3----2.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.138 Å0.142 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 1.8→63.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5461 0 148 566 6175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195789
X-RAY DIFFRACTIONr_bond_other_d0.0010.025534
X-RAY DIFFRACTIONr_angle_refined_deg1.48327884
X-RAY DIFFRACTIONr_angle_other_deg0.776312770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1495726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94924.978231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16115962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6471527
X-RAY DIFFRACTIONr_chiral_restr0.0810.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021210
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_it1.4922.682874
X-RAY DIFFRACTIONr_mcbond_other1.4892.6792873
X-RAY DIFFRACTIONr_mcangle_it2.1534.0133592
X-RAY DIFFRACTIONr_mcangle_other2.2844.1163593
X-RAY DIFFRACTIONr_scbond_it1.9412.9762915
X-RAY DIFFRACTIONr_scbond_other2.1053.0882934
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2974.5134311
X-RAY DIFFRACTIONr_long_range_B_refined5.27923.2776778
X-RAY DIFFRACTIONr_long_range_B_other5.11122.946573
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 242 -
Rwork0.257 4568 -
obs--97.53 %

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