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- PDB-3pzb: Crystals Structure of Aspartate beta-Semialdehyde Dehydrogenase c... -

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Basic information

Entry
Database: PDB / ID: 3pzb
TitleCrystals Structure of Aspartate beta-Semialdehyde Dehydrogenase complex with NADP and D-2,3-Diaminopropionate
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / NADP / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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-amino-D-alanine / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsPavlovsky, A.G. / Viola, R.E.
CitationJournal: Chem.Biol.Drug Des. / Year: 2012
Title: Structural Characterization of Inhibitors with Selectivity against Members of a Homologous Enzyme Family.
Authors: Pavlovsky, A.G. / Liu, X. / Faehnle, C.R. / Potente, N. / Viola, R.E.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Non-polymer description
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 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_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)82,10512
Polymers80,0772
Non-polymers2,02810
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-26 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.042, 100.090, 64.483
Angle α, β, γ (deg.)90.00, 100.81, 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


Mass: 40038.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: CGSSp23BS72_03388 / Plasmid: pET 28a / 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, 443 molecules

#2: Chemical ChemComp-2RA / 3-amino-D-alanine / diaminopropanoic acid


Type: D-peptide linking / Mass: 104.108 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8N2O2
#3: 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
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 23% PEG 8K, 0.1 M tris-HCL, 0.1 M Na-acetate, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 3, 2009
Details: Horizontally and vertically focusing bimorph mirrors in Kirkpatrick-Baez configuration
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→23 Å / Num. obs: 46990 / % possible obs: 93.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 19.2 Å2 / Rsym value: 0.09 / Net I/σ(I): 10.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 1738 / Rsym value: 0.218 / % possible all: 70.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→23 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.527 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20818 2387 5.1 %RANDOM
Rwork0.17734 ---
obs0.17889 44587 92.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.881 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.27 Å2
2--1.71 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 2→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5465 0 131 433 6029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225712
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.9887770
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2425720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56725.065231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09715959
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3771526
X-RAY DIFFRACTIONr_chiral_restr0.0650.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214216
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.211.53589
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.42425805
X-RAY DIFFRACTIONr_scbond_it0.73832123
X-RAY DIFFRACTIONr_scangle_it1.274.51963
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 118 -
Rwork0.216 2367 -
obs--67.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.18480.1281-0.26520.1962-0.19811.3779-0.0112-0.009-0.01970.0086-0.05580.00430.113-0.12530.06710.0232-0.01250.00020.0505-0.01860.0271.60529.324751.776
20.53890.0682-0.37420.1433-0.06920.6857-0.03540.00920.0003-0.00070.0059-0.0078-0.03930.05210.02950.01750.0006-0.00810.03180.00650.018821.167140.046123.3127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 358
2X-RAY DIFFRACTION1A367 - 371
3X-RAY DIFFRACTION1A372 - 555
4X-RAY DIFFRACTION2B2 - 360
5X-RAY DIFFRACTION2B367 - 371
6X-RAY DIFFRACTION2B372 - 620

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