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- PDB-4r51: Crystal complex structure of sp-Aspartate-Semialdehyde-Dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 4r51
TitleCrystal complex structure of sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine dinucleotide phosphate and phthalic acid
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / 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
ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHTHALIC ACID / :
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)82,47619
Polymers80,0772
Non-polymers2,39917
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-17 kcal/mol
Surface area24400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.780, 98.399, 63.973
Angle α, β, γ (deg.)90.00, 102.65, 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 / Fragment: Aspartate-semialdehyde-dehydrogenase
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 , 6 types, 304 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PHT / PHTHALIC ACID


Mass: 166.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O4
#4: 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
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
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 (pH 6.5), 10mM 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 29, 2013
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: 65690 / Num. obs: 64905 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 23.4 Å2 / Rsym value: 0.151 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.8-1.862.72.464460.528198.7
3.88-503.210.265170.103197.4
3.08-3.883.28.564940.13198.7
2.69-3.083.26.665440.196199.3
2.44-2.693.16.165140.239199.6
2.27-2.443.15.265530.277199.7
2.13-2.2735.264800.271199.1
2.03-2.132.94.664960.288198.8
1.94-2.032.84.364400.311198.6
1.86-1.942.83.564210.389198.5

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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: 3PWK

3pwk


Resolution: 1.81→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.594 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.127 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19775 3283 5.1 %RANDOM
Rwork0.17575 ---
obs0.17689 61525 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.955 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.98 Å20 Å2
3----1.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.113 Å0.127 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 1.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5388 0 155 287 5830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195644
X-RAY DIFFRACTIONr_bond_other_d0.0010.025409
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.9897669
X-RAY DIFFRACTIONr_angle_other_deg0.746312471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8275709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52425.044228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11515938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9741526
X-RAY DIFFRACTIONr_chiral_restr0.070.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216298
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021174
X-RAY DIFFRACTIONr_mcbond_it1.0962.4412835
X-RAY DIFFRACTIONr_mcbond_other1.0952.4392832
X-RAY DIFFRACTIONr_mcangle_it1.7623.6553540
X-RAY DIFFRACTIONr_mcangle_other1.7623.6563541
X-RAY DIFFRACTIONr_scbond_it1.6432.7062809
X-RAY DIFFRACTIONr_scbond_other1.6432.7062810
X-RAY DIFFRACTIONr_scangle_other2.6633.9584129
X-RAY DIFFRACTIONr_long_range_B_refined4.1619.9176170
X-RAY DIFFRACTIONr_long_range_B_other4.07419.7786101
LS refinement shellResolution: 1.807→1.854 Å / Rfactor Rfree error: 0.113 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 3283 -
Rwork0.176 4141 -
obs-61525 89.34 %

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