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- PDB-4r4j: Crystal structure of complex sp_ASADH with 3-carboxypropyl-phthal... -

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Basic information

Entry
Database: PDB / ID: 4r4j
TitleCrystal structure of complex sp_ASADH with 3-carboxypropyl-phthalic acid and Nicotinamide Adenine dinucleotide phosphate
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-(3-carboxypropyl)benzene-1,2-dicarboxylic acid / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.51 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 19, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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)83,23015
Polymers80,0772
Non-polymers3,15313
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-27 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.925, 98.842, 64.329
Angle α, β, γ (deg.)90.00, 100.91, 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, 483 molecules

#2: Chemical ChemComp-3JL / 3-(3-carboxypropyl)benzene-1,2-dicarboxylic acid / 3-carboxypropyl-phthalic acid


Mass: 252.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12O6
#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-NA / SODIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 470 / 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: 47.35 %
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 buffer (pH 6.5), 10mM TCEP, 3% Ethylene Glycole, 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 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: 1.5→50 Å / Num. all: 129590 / Num. obs: 106917 / % possible obs: 82.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 14.9 Å2 / Rsym value: 0.073 / Net I/σ(I): 26.1
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueDiffraction-ID% possible all
1.5-1.562.3108300.323183.7
3.12-502.2111390.052184.8
2.48-3.122.2116100.067189.3
2.17-2.482.3118930.081191.4
1.97-2.172.3119210.102192.2
1.83-1.972.3122080.13194.3
1.72-1.832.3124320.165196
1.63-1.722.4124940.206196.4
1.56-1.632.3123900.253196.4

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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: 1.51→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.058 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18997 5246 4.9 %RANDOM
Rwork0.15103 ---
obs0.15295 101648 92.51 %-
all-129590 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.244 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0.52 Å2
2--1.22 Å20 Å2
3----1.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.074 Å-
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å-
Refinement stepCycle: LAST / Resolution: 1.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5461 0 206 470 6137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195806
X-RAY DIFFRACTIONr_bond_other_d0.0010.025534
X-RAY DIFFRACTIONr_angle_refined_deg1.3392.0027915
X-RAY DIFFRACTIONr_angle_other_deg0.746312778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9585730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53725.065231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83915962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0491526
X-RAY DIFFRACTIONr_chiral_restr0.0690.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021210
X-RAY DIFFRACTIONr_mcbond_it1.7871.9212878
X-RAY DIFFRACTIONr_mcbond_other1.7871.922877
X-RAY DIFFRACTIONr_mcangle_it2.0662.893598
X-RAY DIFFRACTIONr_mcangle_other2.0662.8913599
X-RAY DIFFRACTIONr_scbond_it2.3782.2262928
X-RAY DIFFRACTIONr_scbond_other2.3782.2272929
X-RAY DIFFRACTIONr_scangle_other2.7723.2324310
X-RAY DIFFRACTIONr_long_range_B_refined2.99916.5556691
X-RAY DIFFRACTIONr_long_range_B_other2.91716.2286479
X-RAY DIFFRACTIONr_rigid_bond_restr2.044311340
X-RAY DIFFRACTIONr_sphericity_free20.3765116
X-RAY DIFFRACTIONr_sphericity_bonded8.267511584
LS refinement shellResolution: 1.508→1.547 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 380 -
Rwork0.197 7323 -
obs--90.7 %

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