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- PDB-4r3n: Crystal structure of the ternary complex of sp-ASADH with NADP an... -

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Basic information

Entry
Database: PDB / ID: 4r3n
TitleCrystal structure of the ternary complex of sp-ASADH with NADP and 1,2,3-Benzenetricarboxylic acid
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / protein-nadp-ligand complex / Dehydrogenase / NADP binding
Function / homology
Function and homology information


aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / isoleucine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity
Similarity search - Function
Aspartate-semialdehyde dehydrogenase, beta-type / Aspartate-semialdehyde dehydrogenase / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Aspartate-semialdehyde dehydrogenase, beta-type / Aspartate-semialdehyde dehydrogenase / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
benzene-1,2,3-tricarboxylic acid / ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.35 Å
AuthorsPavlovsky, A.G. / 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 16, 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)83,34319
Polymers80,0772
Non-polymers3,26617
Water6,287349
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11040 Å2
ΔGint-50 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.536, 97.658, 63.978
Angle α, β, γ (deg.)90.00, 102.55, 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: cell / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: asd / Plasmid: pER28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8DQ00, aspartate-semialdehyde dehydrogenase

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Non-polymers , 6 types, 366 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-3GQ / benzene-1,2,3-tricarboxylic acid


Mass: 210.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6O6
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15-22% PEG 3350, 0.1 M sodium acetate, 0.1 M MES (pH 6.5), 3% Ethylene glycol, 10 mM TCEP, 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: Nov 27, 2012
Details: double crystal monochromator and K-B pair of biomorph mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 155700 / Num. obs: 148393 / % possible obs: 95.3 % / Observed criterion σ(I): 1.3 / Redundancy: 3.2 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.061 / Net I/σ(I): 18.85
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.35-1.41.31.3101120.538165.3
2.91-503.632.9157090.039197.7
1.6-1.73.57155080.201199.9
1.52-1.63.49.3154800.279199.8
1.45-1.523.33.3154400.402199.4
1.4-1.452.32138470.484189.1

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.35→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.968 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1613 7440 5 %RANDOM
Rwork0.13071 ---
obs0.13225 140914 95.12 %-
all-148393 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.243 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-1.05 Å2
2--0.45 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5366 0 213 349 5928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195740
X-RAY DIFFRACTIONr_bond_other_d0.0010.025442
X-RAY DIFFRACTIONr_angle_refined_deg1.6472.0037826
X-RAY DIFFRACTIONr_angle_other_deg0.808312557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1185719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28724.978229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70415946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1441527
X-RAY DIFFRACTIONr_chiral_restr0.0890.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216409
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021201
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_it2.2731.6242839
X-RAY DIFFRACTIONr_mcbond_other2.2551.6232834
X-RAY DIFFRACTIONr_mcangle_it2.9932.453545
X-RAY DIFFRACTIONr_mcangle_other2.9952.4513546
X-RAY DIFFRACTIONr_scbond_it4.1192.0532901
X-RAY DIFFRACTIONr_scbond_other4.1192.0542902
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8082.9254274
X-RAY DIFFRACTIONr_long_range_B_refined4.83214.5836390
X-RAY DIFFRACTIONr_long_range_B_other4.83214.5856391
X-RAY DIFFRACTIONr_rigid_bond_restr2.814311182
X-RAY DIFFRACTIONr_sphericity_free42.1135135
X-RAY DIFFRACTIONr_sphericity_bonded14.636511292
LS refinement shellResolution: 1.351→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 356 -
Rwork0.307 6481 -
obs--59.13 %

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