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- PDB-4r54: Complex crystal structure of sp-Aspartate-Semialdehyde-Dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 4r54
TitleComplex crystal structure of sp-Aspartate-Semialdehyde-Dehydrogenase with 3-carboxy-ethyl-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
3-(2-carboxyethyl)benzene-1,2-dicarboxylic acid / ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.81 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 20, 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_atom_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_atom_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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)82,73311
Polymers80,0772
Non-polymers2,6559
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-60 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.537, 98.806, 64.098
Angle α, β, γ (deg.)90.00, 101.16, 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
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, 271 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-3JM / 3-(2-carboxyethyl)benzene-1,2-dicarboxylic acid / 3-carboxy-ethyl-phthalic acid


Mass: 238.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 46.75 %
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 (pH 6.5), 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: Apr 18, 2014
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: 1.8→50 Å / Num. all: 66237 / Num. obs: 65575 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 29.5 Å2 / Rsym value: 0.12 / Net I/σ(I): 26
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueDiffraction-ID% possible all
1.81-1.874.464040.808197.3
3.9-504.567110.082199.5
3.09-3.94.465860.113199.3
2.7-3.094.665880.132199.3
2.46-2.74.765550.147199.2
2.28-2.464.765760.182199.2
2.15-2.284.765670.23199.3
2.04-2.154.765460.303199.1
1.95-2.044.765260.406198.9
1.87-1.954.665160.557198.6

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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: 1.81→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.884 / SU ML: 0.113 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.133 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21946 3303 5 %RANDOM
Rwork0.18377 ---
obs0.18565 62262 98.68 %-
all-65575 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.715 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å22.05 Å2
2--1.56 Å20 Å2
3----3.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.125 Å0.133 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 1.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5448 0 172 262 5882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195769
X-RAY DIFFRACTIONr_bond_other_d0.0010.025497
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9987872
X-RAY DIFFRACTIONr_angle_other_deg0.745312688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9725726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09624.914232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02115963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5311528
X-RAY DIFFRACTIONr_chiral_restr0.0740.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216436
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021211
X-RAY DIFFRACTIONr_mcbond_it1.8293.6952873
X-RAY DIFFRACTIONr_mcbond_other1.8263.6932870
X-RAY DIFFRACTIONr_mcangle_it2.5625.5333590
X-RAY DIFFRACTIONr_mcangle_other2.5625.5343591
X-RAY DIFFRACTIONr_scbond_it2.4014.0352896
X-RAY DIFFRACTIONr_scbond_other2.44.0352893
X-RAY DIFFRACTIONr_scangle_other3.7175.9324274
X-RAY DIFFRACTIONr_long_range_B_refined5.02429.9966422
X-RAY DIFFRACTIONr_long_range_B_other5.02429.9996423
LS refinement shellResolution: 1.808→1.855 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 227 -
Rwork0.306 4316 -
obs--93.17 %

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