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- PDB-4r3w: Crystal Structure Analysis of the 1,2,3-tricarboxylate benzoic ac... -

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Basic information

Entry
Database: PDB / ID: 4r3w
TitleCrystal Structure Analysis of the 1,2,3-tricarboxylate benzoic acid bound to sp-ASADH-2'5'-ADP complex
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / Nicotineamid-dinucleotide
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
benzene-1,2,3-tricarboxylic acid / ADENOSINE-2'-5'-DIPHOSPHATE / ACETATE ION / :
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.91 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 18, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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)81,70416
Polymers80,0772
Non-polymers1,62714
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-40 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.964, 98.444, 64.263
Angle α, β, γ (deg.)90.00, 102.43, 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 , 6 types, 194 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-3GQ / benzene-1,2,3-tricarboxylic acid


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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-A2P / ADENOSINE-2'-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 46.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15-22% PEG, 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: 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: 1.9→50 Å / Num. all: 55400 / Num. obs: 49341 / % possible obs: 87 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Rsym value: 0.074 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID
1.9-1.972.22.80.3011
4.09-503.121.60.0391
2.25-2.392.64.60.1621
2.14-2.252.44.40.1731
2.05-2.142.43.70.2081
1.97-2.052.43.40.2381

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Processing

Software
NameVersionClassification
Blue-raydata collection
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3PWK

3pwk


Resolution: 1.91→62.76 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.379 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22892 2490 5 %RANDOM
Rwork0.18587 ---
obs0.188 46838 86.63 %-
all-56700 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.345 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20.82 Å2
2--2.64 Å20 Å2
3----3.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.049 Å0.185 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.164 Å
Refinement stepCycle: LAST / Resolution: 1.91→62.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5366 0 104 180 5650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195577
X-RAY DIFFRACTIONr_bond_other_d0.0010.025353
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9797579
X-RAY DIFFRACTIONr_angle_other_deg0.76312344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1155708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29325.022227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72915935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9181526
X-RAY DIFFRACTIONr_chiral_restr0.0750.2880
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216261
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021155
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_it1.8333.5992827
X-RAY DIFFRACTIONr_mcbond_other1.8323.5982825
X-RAY DIFFRACTIONr_mcangle_it2.7615.3893533
X-RAY DIFFRACTIONr_mcangle_other2.7245.3813534
X-RAY DIFFRACTIONr_scbond_it2.323.8722750
X-RAY DIFFRACTIONr_scbond_other2.3253.8922693
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6695.7053956
X-RAY DIFFRACTIONr_long_range_B_refined4.95428.586029
X-RAY DIFFRACTIONr_long_range_B_other4.91928.5215984
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.905→1.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 133 -
Rwork0.262 2323 -
obs--58.38 %

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